Mercurial > repos > blankenberg > test
changeset 0:46f45544839f draft
Uploaded
| author | blankenberg |
|---|---|
| date | Wed, 25 Nov 2020 01:57:54 +0000 |
| parents | |
| children | 2a8c426ab5bc |
| files | plink2.xml |
| diffstat | 1 files changed, 8535 insertions(+), 0 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plink2.xml Wed Nov 25 01:57:54 2020 +0000 @@ -0,0 +1,8535 @@ +<tool id="plink2" name="PLINK 2" version="2.00a2.3"> + <requirements> + <requirement type="package" version="2.00a2.3">plink</requirement> + </requirements> + <code file="plink_code_file.py" /> + <stdio> + <exit_code range="1:" /> + </stdio> + <version_command>plink2 --version</version_command> + <command><![CDATA[ + plink2 + +#if str($CONDITIONAL_pfile.CONDITIONAL_SELECT_pfile) == "set": + --pfile + + + #if $str($CONDITIONAL_pfile.pfile_MOD_0_0): + '${CONDITIONAL_pfile.pfile_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_pfile.pfile_MOD_1_0): + '${CONDITIONAL_pfile.pfile_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_pgen.CONDITIONAL_SELECT_pgen) == "set": + --pgen + + + #if $CONDITIONAL_pgen.pgen_MOD_0_0: + '${CONDITIONAL_pgen.pgen_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_pvar.CONDITIONAL_SELECT_pvar) == "set": + --pvar + + + #if $CONDITIONAL_pvar.pvar_MOD_0_0: + '${CONDITIONAL_pvar.pvar_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_psam.CONDITIONAL_SELECT_psam) == "set": + --psam + + + #if $CONDITIONAL_psam.psam_MOD_0_0: + '${CONDITIONAL_psam.psam_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_bpfile.CONDITIONAL_SELECT_bpfile) == "set": + --bpfile + + + #if $str($CONDITIONAL_bpfile.bpfile_MOD_0_0): + '${CONDITIONAL_bpfile.bpfile_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_bpfile.bpfile_MOD_1_0): + '${CONDITIONAL_bpfile.bpfile_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_autoconv.CONDITIONAL_SELECT_keep_autoconv) == "set": + --keep-autoconv + + +#end if + +#if str($CONDITIONAL_no_fid.CONDITIONAL_SELECT_no_fid) == "set": + --no-fid + + +#end if + +#if str($CONDITIONAL_no_parents.CONDITIONAL_SELECT_no_parents) == "set": + --no-parents + + +#end if + +#if str($CONDITIONAL_no_sex.CONDITIONAL_SELECT_no_sex) == "set": + --no-sex + + +#end if + +#if str($CONDITIONAL_vcf.CONDITIONAL_SELECT_vcf) == "set": + --vcf + + + #if $CONDITIONAL_vcf.vcf_MOD_0_0: + '${CONDITIONAL_vcf.vcf_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_vcf.vcf_MOD_1_0): + '${CONDITIONAL_vcf.vcf_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_bcf.CONDITIONAL_SELECT_bcf) == "set": + --bcf + + + #if $CONDITIONAL_bcf.bcf_MOD_0_0: + '${CONDITIONAL_bcf.bcf_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_bcf.bcf_MOD_1_0): + '${CONDITIONAL_bcf.bcf_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_bgen.CONDITIONAL_SELECT_bgen) == "set": + --bgen + + + #if $CONDITIONAL_bgen.bgen_MOD_0_0: + '${CONDITIONAL_bgen.bgen_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_bgen.bgen_MOD_1_0): + '${CONDITIONAL_bgen.bgen_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_bgen.bgen_MOD_2_0): + '${CONDITIONAL_bgen.bgen_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_gen.CONDITIONAL_SELECT_gen) == "set": + --gen + + + #if $CONDITIONAL_gen.gen_MOD_0_0: + '${CONDITIONAL_gen.gen_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_gen.gen_MOD_1_0): + '${CONDITIONAL_gen.gen_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_sample.CONDITIONAL_SELECT_sample) == "set": + --sample + + + #if $CONDITIONAL_sample.sample_MOD_0_0: + '${CONDITIONAL_sample.sample_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_haps.CONDITIONAL_SELECT_haps) == "set": + --haps + + + #if $CONDITIONAL_haps.haps_MOD_0_0: + '${CONDITIONAL_haps.haps_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_haps.CONDITIONAL_haps_MOD_1.CONDITIONAL_SELECT_haps_MOD_1) == 'from_list' + '${CONDITIONAL_haps.CONDITIONAL_haps_MOD_1.haps_MOD_1}' + #end if + + +#end if + +#if str($CONDITIONAL_legend.CONDITIONAL_SELECT_legend) == "set": + --legend + + + #if $CONDITIONAL_legend.legend_MOD_0_0: + '${CONDITIONAL_legend.legend_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_legend.legend_MOD_1_0): + '${CONDITIONAL_legend.legend_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_map.CONDITIONAL_SELECT_map) == "set": + --map + + + #if $CONDITIONAL_map.map_MOD_0_0: + '${CONDITIONAL_map.map_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_import_dosage.CONDITIONAL_SELECT_import_dosage) == "set": + --import-dosage + + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_0_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_1_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_2_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_3_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_4_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_4_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_5_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_5_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_6_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_6_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_7_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_7_0}' + #end if + +#if $str($CONDITIONAL_import_dosage.CONDITIONAL_import_dosage_MOD_8.CONDITIONAL_SELECT_import_dosage_MOD_8) == 'from_list' + '${CONDITIONAL_import_dosage.CONDITIONAL_import_dosage_MOD_8.import_dosage_MOD_8}' + #end if + + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_9_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_9_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_10_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_10_0}' + #end if + + #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_11_0): + '${CONDITIONAL_import_dosage.import_dosage_MOD_11_0}' + #end if + +#end if + +#if str($CONDITIONAL_dummy.CONDITIONAL_SELECT_dummy) == "set": + --dummy + + + #if $str($CONDITIONAL_dummy.dummy_MOD_0_0): + '${CONDITIONAL_dummy.dummy_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_dummy.dummy_MOD_1_0): + '${CONDITIONAL_dummy.dummy_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_dummy.dummy_MOD_2_0): + '${CONDITIONAL_dummy.dummy_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_dummy.dummy_MOD_3_0): + '${CONDITIONAL_dummy.dummy_MOD_3_0}' + #end if + +#if $str($CONDITIONAL_dummy.CONDITIONAL_dummy_MOD_4.CONDITIONAL_SELECT_dummy_MOD_4) == 'from_list' + '${CONDITIONAL_dummy.CONDITIONAL_dummy_MOD_4.dummy_MOD_4}' + #end if + + + #if $str($CONDITIONAL_dummy.dummy_MOD_5_0): + '${CONDITIONAL_dummy.dummy_MOD_5_0}' + #end if + + #if $str($CONDITIONAL_dummy.dummy_MOD_6_0): + '${CONDITIONAL_dummy.dummy_MOD_6_0}' + #end if + + #if $str($CONDITIONAL_dummy.dummy_MOD_7_0): + '${CONDITIONAL_dummy.dummy_MOD_7_0}' + #end if + +#end if + +#if str($CONDITIONAL_fa.CONDITIONAL_SELECT_fa) == "set": + --fa + + + #if $CONDITIONAL_fa.fa_MOD_0_0: + '${CONDITIONAL_fa.fa_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_rm_dup.CONDITIONAL_SELECT_rm_dup) == "set": + --rm-dup + + + #if $str($CONDITIONAL_rm_dup.rm_dup_MOD_0_0): + '${CONDITIONAL_rm_dup.rm_dup_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_rm_dup.rm_dup_MOD_1_0): + '${CONDITIONAL_rm_dup.rm_dup_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_pgen.CONDITIONAL_SELECT_make_pgen) == "set": + --make-pgen + + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_0_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_1_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_2_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_3_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_4_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_4_0}' + #end if + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_5_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_5_0}' + #end if + + #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_6_0): + '${CONDITIONAL_make_pgen.make_pgen_MOD_6_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_bpgen.CONDITIONAL_SELECT_make_bpgen) == "set": + --make-bpgen + + + #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_0_0): + '${CONDITIONAL_make_bpgen.make_bpgen_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_1_0): + '${CONDITIONAL_make_bpgen.make_bpgen_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_2_0): + '${CONDITIONAL_make_bpgen.make_bpgen_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_3_0): + '${CONDITIONAL_make_bpgen.make_bpgen_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_4_0): + '${CONDITIONAL_make_bpgen.make_bpgen_MOD_4_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_bed.CONDITIONAL_SELECT_make_bed) == "set": + --make-bed + + + #if $str($CONDITIONAL_make_bed.make_bed_MOD_0_0): + '${CONDITIONAL_make_bed.make_bed_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_bed.make_bed_MOD_1_0): + '${CONDITIONAL_make_bed.make_bed_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_just_pvar.CONDITIONAL_SELECT_make_just_pvar) == "set": + --make-just-pvar + + + #if $str($CONDITIONAL_make_just_pvar.make_just_pvar_MOD_0_0): + '${CONDITIONAL_make_just_pvar.make_just_pvar_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_just_pvar.make_just_pvar_MOD_1_0): + '${CONDITIONAL_make_just_pvar.make_just_pvar_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_just_psam.CONDITIONAL_SELECT_make_just_psam) == "set": + --make-just-psam + + + #if $str($CONDITIONAL_make_just_psam.make_just_psam_MOD_0_0): + '${CONDITIONAL_make_just_psam.make_just_psam_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_just_bim.CONDITIONAL_SELECT_make_just_bim) == "set": + --make-just-bim + + + #if $str($CONDITIONAL_make_just_bim.make_just_bim_MOD_0_0): + '${CONDITIONAL_make_just_bim.make_just_bim_MOD_0_0}' + #end if + +#end if + +${make_just_fam} + +#if str($CONDITIONAL_export.CONDITIONAL_SELECT_export) == "set": + --export + + + #if $str($CONDITIONAL_export.export_MOD_0_0): + '${CONDITIONAL_export.export_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_export.CONDITIONAL_export_MOD_1.CONDITIONAL_SELECT_export_MOD_1) == 'from_list' + '${CONDITIONAL_export.CONDITIONAL_export_MOD_1.export_MOD_1}' + #end if + + + #if $str($CONDITIONAL_export.export_MOD_2_0): + '${CONDITIONAL_export.export_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_3_0): + '${CONDITIONAL_export.export_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_4_0): + '${CONDITIONAL_export.export_MOD_4_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_5_0): + '${CONDITIONAL_export.export_MOD_5_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_6_0): + '${CONDITIONAL_export.export_MOD_6_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_7_0): + '${CONDITIONAL_export.export_MOD_7_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_8_0): + '${CONDITIONAL_export.export_MOD_8_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_9_0): + '${CONDITIONAL_export.export_MOD_9_0}' + #end if + + #if $str($CONDITIONAL_export.export_MOD_10_0): + '${CONDITIONAL_export.export_MOD_10_0}' + #end if + +#end if + +#if str($CONDITIONAL_freq.CONDITIONAL_SELECT_freq) == "set": + --freq + + + #if $str($CONDITIONAL_freq.freq_MOD_0_0): + '${CONDITIONAL_freq.freq_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_freq.freq_MOD_1_0): + '${CONDITIONAL_freq.freq_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_freq.freq_MOD_2_0): + '${CONDITIONAL_freq.freq_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_freq.freq_MOD_3_0): + '${CONDITIONAL_freq.freq_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_geno_counts.CONDITIONAL_SELECT_geno_counts) == "set": + --geno-counts + + + #if $str($CONDITIONAL_geno_counts.geno_counts_MOD_0_0): + '${CONDITIONAL_geno_counts.geno_counts_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_geno_counts.geno_counts_MOD_1_0): + '${CONDITIONAL_geno_counts.geno_counts_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_sample_counts.CONDITIONAL_SELECT_sample_counts) == "set": + --sample-counts + + + #if $str($CONDITIONAL_sample_counts.sample_counts_MOD_0_0): + '${CONDITIONAL_sample_counts.sample_counts_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_sample_counts.sample_counts_MOD_1_0): + '${CONDITIONAL_sample_counts.sample_counts_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_missing.CONDITIONAL_SELECT_missing) == "set": + --missing + + + #if $str($CONDITIONAL_missing.missing_MOD_0_0): + '${CONDITIONAL_missing.missing_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_missing.CONDITIONAL_missing_MOD_1.CONDITIONAL_SELECT_missing_MOD_1) == 'from_list' + '${CONDITIONAL_missing.CONDITIONAL_missing_MOD_1.missing_MOD_1}' + #end if + + + #if $str($CONDITIONAL_missing.missing_MOD_2_0): + '${CONDITIONAL_missing.missing_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_missing.missing_MOD_3_0): + '${CONDITIONAL_missing.missing_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_hardy.CONDITIONAL_SELECT_hardy) == "set": + --hardy + + + #if $str($CONDITIONAL_hardy.hardy_MOD_0_0): + '${CONDITIONAL_hardy.hardy_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_hardy.hardy_MOD_1_0): + '${CONDITIONAL_hardy.hardy_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_hardy.hardy_MOD_2_0): + '${CONDITIONAL_hardy.hardy_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_hardy.hardy_MOD_3_0): + '${CONDITIONAL_hardy.hardy_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_indep_pairwise.CONDITIONAL_SELECT_indep_pairwise) == "set": + --indep-pairwise + + + #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_0_0): + '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_1_0): + '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_2_0): + '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_3_0): + '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_ld.CONDITIONAL_SELECT_ld) == "set": + --ld + + + #if $str($CONDITIONAL_ld.ld_MOD_0_0): + '${CONDITIONAL_ld.ld_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_ld.ld_MOD_1_0): + '${CONDITIONAL_ld.ld_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_ld.ld_MOD_2_0): + '${CONDITIONAL_ld.ld_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_ld.ld_MOD_3_0): + '${CONDITIONAL_ld.ld_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_OVERLOADED_SELECT_sample_diff) == "form_0": + #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_SELECT_sample_diff) == "set": + --sample-diff + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.CONDITIONAL_SELECT_sample_diff_MOD_1) == 'from_list' + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.sample_diff_MOD_1}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.CONDITIONAL_SELECT_sample_diff_MOD_3) == 'from_list' + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.sample_diff_MOD_3}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_8.CONDITIONAL_SELECT_sample_diff_MOD_8) == 'from_list' + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_8.sample_diff_MOD_8}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_9_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_9_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_10_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_10_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_OVERLOADED_SELECT_sample_diff) == "form_1": + #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_SELECT_sample_diff) == "set": + --sample-diff + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.CONDITIONAL_SELECT_sample_diff_MOD_1) == 'from_list' + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.sample_diff_MOD_1}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.CONDITIONAL_SELECT_sample_diff_MOD_3) == 'from_list' + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.sample_diff_MOD_3}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_8_0): + '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_8_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_make_king.CONDITIONAL_SELECT_make_king) == "set": + --make-king + + +#if $str($CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_0.CONDITIONAL_SELECT_make_king_MOD_0) == 'from_list' + '${CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_0.make_king_MOD_0}' + #end if + + +#if $str($CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_1.CONDITIONAL_SELECT_make_king_MOD_1) == 'from_list' + '${CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_1.make_king_MOD_1}' + #end if + + +#end if + +#if str($CONDITIONAL_make_king_table.CONDITIONAL_SELECT_make_king_table) == "set": + --make-king-table + + + #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_0_0): + '${CONDITIONAL_make_king_table.make_king_table_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_1_0): + '${CONDITIONAL_make_king_table.make_king_table_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_2_0): + '${CONDITIONAL_make_king_table.make_king_table_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_3_0): + '${CONDITIONAL_make_king_table.make_king_table_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_make_rel.CONDITIONAL_SELECT_make_rel) == "set": + --make-rel + + + #if $str($CONDITIONAL_make_rel.make_rel_MOD_0_0): + '${CONDITIONAL_make_rel.make_rel_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_rel.make_rel_MOD_1_0): + '${CONDITIONAL_make_rel.make_rel_MOD_1_0}' + #end if + +#if $str($CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_2.CONDITIONAL_SELECT_make_rel_MOD_2) == 'from_list' + '${CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_2.make_rel_MOD_2}' + #end if + + +#if $str($CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_3.CONDITIONAL_SELECT_make_rel_MOD_3) == 'from_list' + '${CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_3.make_rel_MOD_3}' + #end if + + +#end if + +#if str($CONDITIONAL_make_grm_list.CONDITIONAL_SELECT_make_grm_list) == "set": + --make-grm-list + + + #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_0_0): + '${CONDITIONAL_make_grm_list.make_grm_list_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_1_0): + '${CONDITIONAL_make_grm_list.make_grm_list_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_2_0): + '${CONDITIONAL_make_grm_list.make_grm_list_MOD_2_0}' + #end if + +#if $str($CONDITIONAL_make_grm_list.CONDITIONAL_make_grm_list_MOD_3.CONDITIONAL_SELECT_make_grm_list_MOD_3) == 'from_list' + '${CONDITIONAL_make_grm_list.CONDITIONAL_make_grm_list_MOD_3.make_grm_list_MOD_3}' + #end if + + +#end if + +#if str($CONDITIONAL_make_grm_bin.CONDITIONAL_SELECT_make_grm_bin) == "set": + --make-grm-bin + + + #if $str($CONDITIONAL_make_grm_bin.make_grm_bin_MOD_0_0): + '${CONDITIONAL_make_grm_bin.make_grm_bin_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_make_grm_bin.make_grm_bin_MOD_1_0): + '${CONDITIONAL_make_grm_bin.make_grm_bin_MOD_1_0}' + #end if + +#if $str($CONDITIONAL_make_grm_bin.CONDITIONAL_make_grm_bin_MOD_2.CONDITIONAL_SELECT_make_grm_bin_MOD_2) == 'from_list' + '${CONDITIONAL_make_grm_bin.CONDITIONAL_make_grm_bin_MOD_2.make_grm_bin_MOD_2}' + #end if + + +#end if + +#if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_OVERLOADED_SELECT_pca) == "form_0": + #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_SELECT_pca) == "set": + --pca + + #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_0_0): + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_0_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_1.CONDITIONAL_SELECT_pca_MOD_1) == 'from_list' + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_1.pca_MOD_1}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_2_0): + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_2_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_OVERLOADED_SELECT_pca) == "form_1": + #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_SELECT_pca) == "set": + --pca + +#if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_0.CONDITIONAL_SELECT_pca_MOD_0) == 'from_list' + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_0.pca_MOD_0}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_1_0): + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_1_0}' + #end if +#if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_2.CONDITIONAL_SELECT_pca_MOD_2) == 'from_list' + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_2.pca_MOD_2}' + #end if + + #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_3_0): + '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_3_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_king_cutoff.CONDITIONAL_SELECT_king_cutoff) == "set": + --king-cutoff + + + #if $str($CONDITIONAL_king_cutoff.king_cutoff_MOD_0_0): + '${CONDITIONAL_king_cutoff.king_cutoff_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_king_cutoff.king_cutoff_MOD_1_0): + '${CONDITIONAL_king_cutoff.king_cutoff_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_write_covar.CONDITIONAL_SELECT_write_covar) == "set": + --write-covar + + + #if $str($CONDITIONAL_write_covar.write_covar_MOD_0_0): + '${CONDITIONAL_write_covar.write_covar_MOD_0_0}' + #end if + +#end if + +${write_samples} + +#if str($CONDITIONAL_write_snplist.CONDITIONAL_SELECT_write_snplist) == "set": + --write-snplist + + + #if $str($CONDITIONAL_write_snplist.write_snplist_MOD_0_0): + '${CONDITIONAL_write_snplist.write_snplist_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_glm.CONDITIONAL_SELECT_glm) == "set": + --glm + + + #if $str($CONDITIONAL_glm.glm_MOD_0_0): + '${CONDITIONAL_glm.glm_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_glm.glm_MOD_1_0): + '${CONDITIONAL_glm.glm_MOD_1_0}' + #end if + +#if $str($CONDITIONAL_glm.CONDITIONAL_glm_MOD_2.CONDITIONAL_SELECT_glm_MOD_2) == 'from_list' + '${CONDITIONAL_glm.CONDITIONAL_glm_MOD_2.glm_MOD_2}' + #end if + + + #if $str($CONDITIONAL_glm.glm_MOD_3_0): + '${CONDITIONAL_glm.glm_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_glm.glm_MOD_4_0): + '${CONDITIONAL_glm.glm_MOD_4_0}' + #end if + +#end if + +#if str($CONDITIONAL_score.CONDITIONAL_SELECT_score) == "set": + --score + + + #if $CONDITIONAL_score.score_MOD_0_0: + '${CONDITIONAL_score.score_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_score.score_MOD_1_0): + '${CONDITIONAL_score.score_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_score.score_MOD_2_0): + '${CONDITIONAL_score.score_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_score.score_MOD_3_0): + '${CONDITIONAL_score.score_MOD_3_0}' + #end if + +#if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_4.CONDITIONAL_SELECT_score_MOD_4) == 'from_list' + '${CONDITIONAL_score.CONDITIONAL_score_MOD_4.score_MOD_4}' + #end if + + +#if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_5.CONDITIONAL_SELECT_score_MOD_5) == 'from_list' + '${CONDITIONAL_score.CONDITIONAL_score_MOD_5.score_MOD_5}' + #end if + + + #if $str($CONDITIONAL_score.score_MOD_6_0): + '${CONDITIONAL_score.score_MOD_6_0}' + #end if + + #if $str($CONDITIONAL_score.score_MOD_7_0): + '${CONDITIONAL_score.score_MOD_7_0}' + #end if + + #if $str($CONDITIONAL_score.score_MOD_8_0): + '${CONDITIONAL_score.score_MOD_8_0}' + #end if + + #if $str($CONDITIONAL_score.score_MOD_9_0): + '${CONDITIONAL_score.score_MOD_9_0}' + #end if + +#if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_10.CONDITIONAL_SELECT_score_MOD_10) == 'from_list' + '${CONDITIONAL_score.CONDITIONAL_score_MOD_10.score_MOD_10}' + #end if + + + #if $str($CONDITIONAL_score.score_MOD_11_0): + '${CONDITIONAL_score.score_MOD_11_0}' + #end if + +#end if + +#if str($CONDITIONAL_variant_score.CONDITIONAL_SELECT_variant_score) == "set": + --variant-score + + + #if $CONDITIONAL_variant_score.variant_score_MOD_0_0: + '${CONDITIONAL_variant_score.variant_score_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_variant_score.variant_score_MOD_1_0): + '${CONDITIONAL_variant_score.variant_score_MOD_1_0}' + #end if + +#if $str($CONDITIONAL_variant_score.CONDITIONAL_variant_score_MOD_2.CONDITIONAL_SELECT_variant_score_MOD_2) == 'from_list' + '${CONDITIONAL_variant_score.CONDITIONAL_variant_score_MOD_2.variant_score_MOD_2}' + #end if + + +#end if + +#if str($CONDITIONAL_adjust_file.CONDITIONAL_SELECT_adjust_file) == "set": + --adjust-file + + + #if $CONDITIONAL_adjust_file.adjust_file_MOD_0_0: + '${CONDITIONAL_adjust_file.adjust_file_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_1_0): + '${CONDITIONAL_adjust_file.adjust_file_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_2_0): + '${CONDITIONAL_adjust_file.adjust_file_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_3_0): + '${CONDITIONAL_adjust_file.adjust_file_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_4_0): + '${CONDITIONAL_adjust_file.adjust_file_MOD_4_0}' + #end if + + #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_5_0): + '${CONDITIONAL_adjust_file.adjust_file_MOD_5_0}' + #end if + + #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_6_0): + '${CONDITIONAL_adjust_file.adjust_file_MOD_6_0}' + #end if + +#end if + +#if str($CONDITIONAL_genotyping_rate.CONDITIONAL_SELECT_genotyping_rate) == "set": + --genotyping-rate + + + #if $str($CONDITIONAL_genotyping_rate.genotyping_rate_MOD_0_0): + '${CONDITIONAL_genotyping_rate.genotyping_rate_MOD_0_0}' + #end if + +#end if + +${pgen_info} + +${validate} + +#if str($CONDITIONAL_zst_decompress.CONDITIONAL_SELECT_zst_decompress) == "set": + --zst-decompress + + + #if $str($CONDITIONAL_zst_decompress.zst_decompress_MOD_0_0): + '${CONDITIONAL_zst_decompress.zst_decompress_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_zst_decompress.zst_decompress_MOD_1_0): + '${CONDITIONAL_zst_decompress.zst_decompress_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_silent.CONDITIONAL_SELECT_silent) == "set": + --silent + + +#end if + +#if str($CONDITIONAL_double_id.CONDITIONAL_SELECT_double_id) == "set": + --double-id + + +#end if + +#if str($CONDITIONAL_const_fid.CONDITIONAL_SELECT_const_fid) == "set": + --const-fid + + + #if $str($CONDITIONAL_const_fid.const_fid_MOD_0_0): + '${CONDITIONAL_const_fid.const_fid_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_id_delim.CONDITIONAL_SELECT_id_delim) == "set": + --id-delim + + + #if $str($CONDITIONAL_id_delim.id_delim_MOD_0_0): + '${CONDITIONAL_id_delim.id_delim_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_idspace_to.CONDITIONAL_SELECT_idspace_to) == "set": + --idspace-to + + + #if $str($CONDITIONAL_idspace_to.idspace_to_MOD_0_0): + '${CONDITIONAL_idspace_to.idspace_to_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_iid_sid.CONDITIONAL_SELECT_iid_sid) == "set": + --iid-sid + + +#end if + +#if str($CONDITIONAL_vcf_require_gt.CONDITIONAL_SELECT_vcf_require_gt) == "set": + --vcf-require-gt + + +#end if + +#if str($CONDITIONAL_vcf_min_gq.CONDITIONAL_SELECT_vcf_min_gq) == "set": + --vcf-min-gq + + + #if $str($CONDITIONAL_vcf_min_gq.vcf_min_gq_MOD_0_0): + '${CONDITIONAL_vcf_min_gq.vcf_min_gq_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_vcf_max_dp.CONDITIONAL_SELECT_vcf_max_dp) == "set": + --vcf-max-dp + + + #if $str($CONDITIONAL_vcf_max_dp.vcf_max_dp_MOD_0_0): + '${CONDITIONAL_vcf_max_dp.vcf_max_dp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_vcf_min_dp.CONDITIONAL_SELECT_vcf_min_dp) == "set": + --vcf-min-dp + + + #if $str($CONDITIONAL_vcf_min_dp.vcf_min_dp_MOD_0_0): + '${CONDITIONAL_vcf_min_dp.vcf_min_dp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_vcf_half_call.CONDITIONAL_SELECT_vcf_half_call) == "set": + --vcf-half-call + + + #if $str($CONDITIONAL_vcf_half_call.vcf_half_call_MOD_0_0): + '${CONDITIONAL_vcf_half_call.vcf_half_call_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_oxford_single_chr.CONDITIONAL_SELECT_oxford_single_chr) == "set": + --oxford-single-chr + + + #if $str($CONDITIONAL_oxford_single_chr.oxford_single_chr_MOD_0_0): + '${CONDITIONAL_oxford_single_chr.oxford_single_chr_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_missing_code.CONDITIONAL_SELECT_missing_code) == "set": + --missing-code + + + #if $str($CONDITIONAL_missing_code.missing_code_MOD_0_0): + '${CONDITIONAL_missing_code.missing_code_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_hard_call_threshold.CONDITIONAL_SELECT_hard_call_threshold) == "set": + --hard-call-threshold + + + #if $str($CONDITIONAL_hard_call_threshold.hard_call_threshold_MOD_0_0): + '${CONDITIONAL_hard_call_threshold.hard_call_threshold_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_dosage_erase_threshold.CONDITIONAL_SELECT_dosage_erase_threshold) == "set": + --dosage-erase-threshold + + + #if $str($CONDITIONAL_dosage_erase_threshold.dosage_erase_threshold_MOD_0_0): + '${CONDITIONAL_dosage_erase_threshold.dosage_erase_threshold_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_import_dosage_certainty.CONDITIONAL_SELECT_import_dosage_certainty) == "set": + --import-dosage-certainty + + + #if $str($CONDITIONAL_import_dosage_certainty.import_dosage_certainty_MOD_0_0): + '${CONDITIONAL_import_dosage_certainty.import_dosage_certainty_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_input_missing_genotype.CONDITIONAL_SELECT_input_missing_genotype) == "set": + --input-missing-genotype + + + #if $str($CONDITIONAL_input_missing_genotype.input_missing_genotype_MOD_0_0): + '${CONDITIONAL_input_missing_genotype.input_missing_genotype_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_allow_extra_chr.CONDITIONAL_SELECT_allow_extra_chr) == "set": + --allow-extra-chr + + +#end if + +#if str($CONDITIONAL_chr_set.CONDITIONAL_SELECT_chr_set) == "set": + --chr-set + + + #if $str($CONDITIONAL_chr_set.chr_set_MOD_0_0): + '${CONDITIONAL_chr_set.chr_set_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_chr_set.chr_set_MOD_1_0): + '${CONDITIONAL_chr_set.chr_set_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_chr_set.chr_set_MOD_2_0): + '${CONDITIONAL_chr_set.chr_set_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_chr_set.chr_set_MOD_3_0): + '${CONDITIONAL_chr_set.chr_set_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_chr_set.chr_set_MOD_4_0): + '${CONDITIONAL_chr_set.chr_set_MOD_4_0}' + #end if + +#end if + +#if str($CONDITIONAL_cow.CONDITIONAL_SELECT_cow) == "set": + --cow + + +#end if + +#if str($CONDITIONAL_dog.CONDITIONAL_SELECT_dog) == "set": + --dog + + +#end if + +#if str($CONDITIONAL_horse.CONDITIONAL_SELECT_horse) == "set": + --horse + + +#end if + +#if str($CONDITIONAL_mouse.CONDITIONAL_SELECT_mouse) == "set": + --mouse + + +#end if + +#if str($CONDITIONAL_rice.CONDITIONAL_SELECT_rice) == "set": + --rice + + +#end if + +#if str($CONDITIONAL_sheep.CONDITIONAL_SELECT_sheep) == "set": + --sheep + + +#end if + +#if str($CONDITIONAL_autosome_num.CONDITIONAL_SELECT_autosome_num) == "set": + --autosome-num + + + #if $str($CONDITIONAL_autosome_num.autosome_num_MOD_0_0): + '${CONDITIONAL_autosome_num.autosome_num_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_human.CONDITIONAL_SELECT_human) == "set": + --human + + +#end if + +#if str($CONDITIONAL_chr_override.CONDITIONAL_SELECT_chr_override) == "set": + --chr-override + + + #if $str($CONDITIONAL_chr_override.chr_override_MOD_0_0): + '${CONDITIONAL_chr_override.chr_override_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_var_min_qual.CONDITIONAL_SELECT_var_min_qual) == "set": + --var-min-qual + + + #if $str($CONDITIONAL_var_min_qual.var_min_qual_MOD_0_0): + '${CONDITIONAL_var_min_qual.var_min_qual_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_var_filter.CONDITIONAL_SELECT_var_filter) == "set": + --var-filter + + + #if $str($CONDITIONAL_var_filter.var_filter_MOD_0_0): + '${CONDITIONAL_var_filter.var_filter_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract_if_info.CONDITIONAL_SELECT_extract_if_info) == "set": + --extract-if-info + + + #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_0_0): + '${CONDITIONAL_extract_if_info.extract_if_info_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_1_0): + '${CONDITIONAL_extract_if_info.extract_if_info_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_2_0): + '${CONDITIONAL_extract_if_info.extract_if_info_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_exclude_if_info.CONDITIONAL_SELECT_exclude_if_info) == "set": + --exclude-if-info + + + #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_0_0): + '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_1_0): + '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_2_0): + '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_require_info.CONDITIONAL_SELECT_require_info) == "set": + --require-info + + + #if $str($CONDITIONAL_require_info.require_info_MOD_0_0): + '${CONDITIONAL_require_info.require_info_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_require_no_info.CONDITIONAL_SELECT_require_no_info) == "set": + --require-no-info + + + #if $str($CONDITIONAL_require_no_info.require_no_info_MOD_0_0): + '${CONDITIONAL_require_no_info.require_no_info_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_require_no_info.require_no_info_MOD_1_0): + '${CONDITIONAL_require_no_info.require_no_info_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract_col_cond.CONDITIONAL_SELECT_extract_col_cond) == "set": + --extract-col-cond + + + #if $CONDITIONAL_extract_col_cond.extract_col_cond_MOD_0_0: + '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_1_0): + '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_2_0): + '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_3_0): + '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract_col_cond_match.CONDITIONAL_SELECT_extract_col_cond_match) == "set": + --extract-col-cond-match + + + #if $str($CONDITIONAL_extract_col_cond_match.extract_col_cond_match_MOD_0_0): + '${CONDITIONAL_extract_col_cond_match.extract_col_cond_match_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract_col_cond_mismatch.CONDITIONAL_SELECT_extract_col_cond_mismatch) == "set": + --extract-col-cond-mismatch + + + #if $str($CONDITIONAL_extract_col_cond_mismatch.extract_col_cond_mismatch_MOD_0_0): + '${CONDITIONAL_extract_col_cond_mismatch.extract_col_cond_mismatch_MOD_0_0}' + #end if + +#end if + +${extract_col_cond_substr} + +#if str($CONDITIONAL_extract_col_cond_min.CONDITIONAL_SELECT_extract_col_cond_min) == "set": + --extract-col-cond-min + + + #if $str($CONDITIONAL_extract_col_cond_min.extract_col_cond_min_MOD_0_0): + '${CONDITIONAL_extract_col_cond_min.extract_col_cond_min_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract_col_cond_max.CONDITIONAL_SELECT_extract_col_cond_max) == "set": + --extract-col-cond-max + + + #if $str($CONDITIONAL_extract_col_cond_max.extract_col_cond_max_MOD_0_0): + '${CONDITIONAL_extract_col_cond_max.extract_col_cond_max_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_pheno.CONDITIONAL_SELECT_pheno) == "set": + --pheno + + + #if $str($CONDITIONAL_pheno.pheno_MOD_0_0): + '${CONDITIONAL_pheno.pheno_MOD_0_0}' + #end if + + #if $CONDITIONAL_pheno.pheno_MOD_1_0: + '${CONDITIONAL_pheno.pheno_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_pheno_name.CONDITIONAL_SELECT_pheno_name) == "set": + --pheno-name + + + #if $str($CONDITIONAL_pheno_name.pheno_name_MOD_0_0): + '${CONDITIONAL_pheno_name.pheno_name_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_pheno_col_nums.CONDITIONAL_SELECT_pheno_col_nums) == "set": + --pheno-col-nums + + + #if $str($CONDITIONAL_pheno_col_nums.pheno_col_nums_MOD_0_0): + '${CONDITIONAL_pheno_col_nums.pheno_col_nums_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_no_psam_pheno.CONDITIONAL_SELECT_no_psam_pheno) == "set": + --no-psam-pheno + + +#end if + +#if str($CONDITIONAL_strict_sid0.CONDITIONAL_SELECT_strict_sid0) == "set": + --strict-sid0 + + +#end if + +#if str($CONDITIONAL_input_missing_phenotype.CONDITIONAL_SELECT_input_missing_phenotype) == "set": + --input-missing-phenotype + + + #if $str($CONDITIONAL_input_missing_phenotype.input_missing_phenotype_MOD_0_0): + '${CONDITIONAL_input_missing_phenotype.input_missing_phenotype_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_no_input_missing_phenotype.CONDITIONAL_SELECT_no_input_missing_phenotype) == "set": + --no-input-missing-phenotype + + +#end if + +#if str($CONDITIONAL_GALAXY_1.CONDITIONAL_SELECT_GALAXY_1) == "set": + --1 + + +#end if + +#if str($CONDITIONAL_missing_catname.CONDITIONAL_SELECT_missing_catname) == "set": + --missing-catname + + + #if $str($CONDITIONAL_missing_catname.missing_catname_MOD_0_0): + '${CONDITIONAL_missing_catname.missing_catname_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_covar.CONDITIONAL_SELECT_covar) == "set": + --covar + + + #if $str($CONDITIONAL_covar.covar_MOD_0_0): + '${CONDITIONAL_covar.covar_MOD_0_0}' + #end if + + #if $CONDITIONAL_covar.covar_MOD_1_0: + '${CONDITIONAL_covar.covar_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_covar_name.CONDITIONAL_SELECT_covar_name) == "set": + --covar-name + + + #if $str($CONDITIONAL_covar_name.covar_name_MOD_0_0): + '${CONDITIONAL_covar_name.covar_name_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_covar_col_nums.CONDITIONAL_SELECT_covar_col_nums) == "set": + --covar-col-nums + + + #if $str($CONDITIONAL_covar_col_nums.covar_col_nums_MOD_0_0): + '${CONDITIONAL_covar_col_nums.covar_col_nums_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_within.CONDITIONAL_SELECT_within) == "set": + --within + + + #if $CONDITIONAL_within.within_MOD_0_0: + '${CONDITIONAL_within.within_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_within.within_MOD_1_0): + '${CONDITIONAL_within.within_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_mwithin.CONDITIONAL_SELECT_mwithin) == "set": + --mwithin + + + #if $str($CONDITIONAL_mwithin.mwithin_MOD_0_0): + '${CONDITIONAL_mwithin.mwithin_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_family.CONDITIONAL_SELECT_family) == "set": + --family + + + #if $str($CONDITIONAL_family.family_MOD_0_0): + '${CONDITIONAL_family.family_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_family_missing_catname.CONDITIONAL_SELECT_family_missing_catname) == "set": + --family-missing-catname + + + #if $str($CONDITIONAL_family_missing_catname.family_missing_catname_MOD_0_0): + '${CONDITIONAL_family_missing_catname.family_missing_catname_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep.CONDITIONAL_SELECT_keep) == "set": + --keep + + + #if $str($CONDITIONAL_keep.keep_MOD_0_0): + '${CONDITIONAL_keep.keep_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_remove.CONDITIONAL_SELECT_remove) == "set": + --remove + + + #if $str($CONDITIONAL_remove.remove_MOD_0_0): + '${CONDITIONAL_remove.remove_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_fam.CONDITIONAL_SELECT_keep_fam) == "set": + --keep-fam + + + #if $str($CONDITIONAL_keep_fam.keep_fam_MOD_0_0): + '${CONDITIONAL_keep_fam.keep_fam_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_remove_fam.CONDITIONAL_SELECT_remove_fam) == "set": + --remove-fam + + + #if $str($CONDITIONAL_remove_fam.remove_fam_MOD_0_0): + '${CONDITIONAL_remove_fam.remove_fam_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract.CONDITIONAL_SELECT_extract) == "set": + --extract + + +#if $str($CONDITIONAL_extract.CONDITIONAL_extract_MOD_0.CONDITIONAL_SELECT_extract_MOD_0) == 'from_list' + '${CONDITIONAL_extract.CONDITIONAL_extract_MOD_0.extract_MOD_0}' + #end if + + + #if $str($CONDITIONAL_extract.extract_MOD_1_0): + '${CONDITIONAL_extract.extract_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_exclude.CONDITIONAL_SELECT_exclude) == "set": + --exclude + + +#if $str($CONDITIONAL_exclude.CONDITIONAL_exclude_MOD_0.CONDITIONAL_SELECT_exclude_MOD_0) == 'from_list' + '${CONDITIONAL_exclude.CONDITIONAL_exclude_MOD_0.exclude_MOD_0}' + #end if + + + #if $str($CONDITIONAL_exclude.exclude_MOD_1_0): + '${CONDITIONAL_exclude.exclude_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_extract_intersect.CONDITIONAL_SELECT_extract_intersect) == "set": + --extract-intersect + + +#if $str($CONDITIONAL_extract_intersect.CONDITIONAL_extract_intersect_MOD_0.CONDITIONAL_SELECT_extract_intersect_MOD_0) == 'from_list' + '${CONDITIONAL_extract_intersect.CONDITIONAL_extract_intersect_MOD_0.extract_intersect_MOD_0}' + #end if + + + #if $str($CONDITIONAL_extract_intersect.extract_intersect_MOD_1_0): + '${CONDITIONAL_extract_intersect.extract_intersect_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_cats.CONDITIONAL_SELECT_keep_cats) == "set": + --keep-cats + + + #if $CONDITIONAL_keep_cats.keep_cats_MOD_0_0: + '${CONDITIONAL_keep_cats.keep_cats_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_cat_names.CONDITIONAL_SELECT_keep_cat_names) == "set": + --keep-cat-names + + + #if $str($CONDITIONAL_keep_cat_names.keep_cat_names_MOD_0_0): + '${CONDITIONAL_keep_cat_names.keep_cat_names_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_cat_pheno.CONDITIONAL_SELECT_keep_cat_pheno) == "set": + --keep-cat-pheno + + + #if $str($CONDITIONAL_keep_cat_pheno.keep_cat_pheno_MOD_0_0): + '${CONDITIONAL_keep_cat_pheno.keep_cat_pheno_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_remove_cats.CONDITIONAL_SELECT_remove_cats) == "set": + --remove-cats + + + #if $CONDITIONAL_remove_cats.remove_cats_MOD_0_0: + '${CONDITIONAL_remove_cats.remove_cats_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_remove_cat_names.CONDITIONAL_SELECT_remove_cat_names) == "set": + --remove-cat-names + + + #if $str($CONDITIONAL_remove_cat_names.remove_cat_names_MOD_0_0): + '${CONDITIONAL_remove_cat_names.remove_cat_names_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_remove_cat_pheno.CONDITIONAL_SELECT_remove_cat_pheno) == "set": + --remove-cat-pheno + + + #if $str($CONDITIONAL_remove_cat_pheno.remove_cat_pheno_MOD_0_0): + '${CONDITIONAL_remove_cat_pheno.remove_cat_pheno_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_split_cat_pheno.CONDITIONAL_SELECT_split_cat_pheno) == "set": + --split-cat-pheno + + +#if $str($CONDITIONAL_split_cat_pheno.CONDITIONAL_split_cat_pheno_MOD_0.CONDITIONAL_SELECT_split_cat_pheno_MOD_0) == 'from_list' + '${CONDITIONAL_split_cat_pheno.CONDITIONAL_split_cat_pheno_MOD_0.split_cat_pheno_MOD_0}' + #end if + + + #if $str($CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_1_0): + '${CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_2_0): + '${CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_loop_cats.CONDITIONAL_SELECT_loop_cats) == "set": + --loop-cats + + + #if $str($CONDITIONAL_loop_cats.loop_cats_MOD_0_0): + '${CONDITIONAL_loop_cats.loop_cats_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_no_id_header.CONDITIONAL_SELECT_no_id_header) == "set": + --no-id-header + + + #if $str($CONDITIONAL_no_id_header.no_id_header_MOD_0_0): + '${CONDITIONAL_no_id_header.no_id_header_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_variance_standardize.CONDITIONAL_SELECT_variance_standardize) == "set": + --variance-standardize + + + #if $str($CONDITIONAL_variance_standardize.variance_standardize_MOD_0_0): + '${CONDITIONAL_variance_standardize.variance_standardize_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_covar_variance_standardize.CONDITIONAL_SELECT_covar_variance_standardize) == "set": + --covar-variance-standardize + + + #if $str($CONDITIONAL_covar_variance_standardize.covar_variance_standardize_MOD_0_0): + '${CONDITIONAL_covar_variance_standardize.covar_variance_standardize_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_quantile_normalize.CONDITIONAL_SELECT_quantile_normalize) == "set": + --quantile-normalize + + + #if $str($CONDITIONAL_quantile_normalize.quantile_normalize_MOD_0_0): + '${CONDITIONAL_quantile_normalize.quantile_normalize_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_pheno_quantile_normalize.CONDITIONAL_SELECT_pheno_quantile_normalize) == "set": + --pheno-quantile-normalize + + + #if $str($CONDITIONAL_pheno_quantile_normalize.pheno_quantile_normalize_MOD_0_0): + '${CONDITIONAL_pheno_quantile_normalize.pheno_quantile_normalize_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_covar_quantile_normalize.CONDITIONAL_SELECT_covar_quantile_normalize) == "set": + --covar-quantile-normalize + + + #if $str($CONDITIONAL_covar_quantile_normalize.covar_quantile_normalize_MOD_0_0): + '${CONDITIONAL_covar_quantile_normalize.covar_quantile_normalize_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_chr.CONDITIONAL_SELECT_chr) == "set": + --chr + + + #if $str($CONDITIONAL_chr.chr_MOD_0_0): + '${CONDITIONAL_chr.chr_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_not_chr.CONDITIONAL_SELECT_not_chr) == "set": + --not-chr + + + #if $str($CONDITIONAL_not_chr.not_chr_MOD_0_0): + '${CONDITIONAL_not_chr.not_chr_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_autosome.CONDITIONAL_SELECT_autosome) == "set": + --autosome + + +#end if + +#if str($CONDITIONAL_autosome_par.CONDITIONAL_SELECT_autosome_par) == "set": + --autosome-par + + +#end if + +#if str($CONDITIONAL_snps_only.CONDITIONAL_SELECT_snps_only) == "set": + --snps-only + + + #if $str($CONDITIONAL_snps_only.snps_only_MOD_0_0): + '${CONDITIONAL_snps_only.snps_only_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_from.CONDITIONAL_SELECT_from) == "set": + --from + + + #if $str($CONDITIONAL_from.from_MOD_0_0): + '${CONDITIONAL_from.from_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_to.CONDITIONAL_SELECT_to) == "set": + --to + + + #if $str($CONDITIONAL_to.to_MOD_0_0): + '${CONDITIONAL_to.to_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_snp.CONDITIONAL_SELECT_snp) == "set": + --snp + + + #if $str($CONDITIONAL_snp.snp_MOD_0_0): + '${CONDITIONAL_snp.snp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_exclude_snp.CONDITIONAL_SELECT_exclude_snp) == "set": + --exclude-snp + + + #if $str($CONDITIONAL_exclude_snp.exclude_snp_MOD_0_0): + '${CONDITIONAL_exclude_snp.exclude_snp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_window.CONDITIONAL_SELECT_window) == "set": + --window + + + #if $str($CONDITIONAL_window.window_MOD_0_0): + '${CONDITIONAL_window.window_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_from_bp.CONDITIONAL_SELECT_from_bp) == "set": + --from-bp + + + #if $str($CONDITIONAL_from_bp.from_bp_MOD_0_0): + '${CONDITIONAL_from_bp.from_bp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_to_bp.CONDITIONAL_SELECT_to_bp) == "set": + --to-bp + + + #if $str($CONDITIONAL_to_bp.to_bp_MOD_0_0): + '${CONDITIONAL_to_bp.to_bp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_from_kb.CONDITIONAL_SELECT_from_kb) == "set": + --from-kb + + + #if $str($CONDITIONAL_from_kb.from_kb_MOD_0_0): + '${CONDITIONAL_from_kb.from_kb_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_to_kb.CONDITIONAL_SELECT_to_kb) == "set": + --to-kb + + + #if $str($CONDITIONAL_to_kb.to_kb_MOD_0_0): + '${CONDITIONAL_to_kb.to_kb_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_from_mb.CONDITIONAL_SELECT_from_mb) == "set": + --from-mb + + + #if $str($CONDITIONAL_from_mb.from_mb_MOD_0_0): + '${CONDITIONAL_from_mb.from_mb_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_to_mb.CONDITIONAL_SELECT_to_mb) == "set": + --to-mb + + + #if $str($CONDITIONAL_to_mb.to_mb_MOD_0_0): + '${CONDITIONAL_to_mb.to_mb_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_snps.CONDITIONAL_SELECT_snps) == "set": + --snps + + + #if $str($CONDITIONAL_snps.snps_MOD_0_0): + '${CONDITIONAL_snps.snps_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_exclude_snps.CONDITIONAL_SELECT_exclude_snps) == "set": + --exclude-snps + + + #if $str($CONDITIONAL_exclude_snps.exclude_snps_MOD_0_0): + '${CONDITIONAL_exclude_snps.exclude_snps_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_force_intersect.CONDITIONAL_SELECT_force_intersect) == "set": + --force-intersect + + +#end if + +#if str($CONDITIONAL_thin.CONDITIONAL_SELECT_thin) == "set": + --thin + + + #if $str($CONDITIONAL_thin.thin_MOD_0_0): + '${CONDITIONAL_thin.thin_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_thin_count.CONDITIONAL_SELECT_thin_count) == "set": + --thin-count + + + #if $str($CONDITIONAL_thin_count.thin_count_MOD_0_0): + '${CONDITIONAL_thin_count.thin_count_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_bp_space.CONDITIONAL_SELECT_bp_space) == "set": + --bp-space + + + #if $str($CONDITIONAL_bp_space.bp_space_MOD_0_0): + '${CONDITIONAL_bp_space.bp_space_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_thin_indiv.CONDITIONAL_SELECT_thin_indiv) == "set": + --thin-indiv + + + #if $str($CONDITIONAL_thin_indiv.thin_indiv_MOD_0_0): + '${CONDITIONAL_thin_indiv.thin_indiv_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_thin_indiv_count.CONDITIONAL_SELECT_thin_indiv_count) == "set": + --thin-indiv-count + + + #if $str($CONDITIONAL_thin_indiv_count.thin_indiv_count_MOD_0_0): + '${CONDITIONAL_thin_indiv_count.thin_indiv_count_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_col_match.CONDITIONAL_SELECT_keep_col_match) == "set": + --keep-col-match + + + #if $CONDITIONAL_keep_col_match.keep_col_match_MOD_0_0: + '${CONDITIONAL_keep_col_match.keep_col_match_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_keep_col_match.keep_col_match_MOD_1_0): + '${CONDITIONAL_keep_col_match.keep_col_match_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_col_match_name.CONDITIONAL_SELECT_keep_col_match_name) == "set": + --keep-col-match-name + + + #if $str($CONDITIONAL_keep_col_match_name.keep_col_match_name_MOD_0_0): + '${CONDITIONAL_keep_col_match_name.keep_col_match_name_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_col_match_num.CONDITIONAL_SELECT_keep_col_match_num) == "set": + --keep-col-match-num + + + #if $str($CONDITIONAL_keep_col_match_num.keep_col_match_num_MOD_0_0): + '${CONDITIONAL_keep_col_match_num.keep_col_match_num_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_geno.CONDITIONAL_SELECT_geno) == "set": + --geno + + + #if $str($CONDITIONAL_geno.geno_MOD_0_0): + '${CONDITIONAL_geno.geno_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_geno.CONDITIONAL_geno_MOD_1.CONDITIONAL_SELECT_geno_MOD_1) == 'from_list' + '${CONDITIONAL_geno.CONDITIONAL_geno_MOD_1.geno_MOD_1}' + #end if + + +#end if + +#if str($CONDITIONAL_mind.CONDITIONAL_SELECT_mind) == "set": + --mind + + + #if $str($CONDITIONAL_mind.mind_MOD_0_0): + '${CONDITIONAL_mind.mind_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_mind.CONDITIONAL_mind_MOD_1.CONDITIONAL_SELECT_mind_MOD_1) == 'from_list' + '${CONDITIONAL_mind.CONDITIONAL_mind_MOD_1.mind_MOD_1}' + #end if + + +#end if + +#if str($CONDITIONAL_require_pheno.CONDITIONAL_SELECT_require_pheno) == "set": + --require-pheno + + + #if $str($CONDITIONAL_require_pheno.require_pheno_MOD_0_0): + '${CONDITIONAL_require_pheno.require_pheno_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_require_covar.CONDITIONAL_SELECT_require_covar) == "set": + --require-covar + + + #if $str($CONDITIONAL_require_covar.require_covar_MOD_0_0): + '${CONDITIONAL_require_covar.require_covar_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_maf.CONDITIONAL_SELECT_maf) == "set": + --maf + + + #if $str($CONDITIONAL_maf.maf_MOD_0_0): + '${CONDITIONAL_maf.maf_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_maf.maf_MOD_1_0): + '${CONDITIONAL_maf.maf_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_max_maf.CONDITIONAL_SELECT_max_maf) == "set": + --max-maf + + + #if $str($CONDITIONAL_max_maf.max_maf_MOD_0_0): + '${CONDITIONAL_max_maf.max_maf_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_max_maf.max_maf_MOD_1_0): + '${CONDITIONAL_max_maf.max_maf_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_mac.CONDITIONAL_SELECT_mac) == "set": + --mac + + + #if $str($CONDITIONAL_mac.mac_MOD_0_0): + '${CONDITIONAL_mac.mac_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_mac.mac_MOD_1_0): + '${CONDITIONAL_mac.mac_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_max_mac.CONDITIONAL_SELECT_max_mac) == "set": + --max-mac + + + #if $str($CONDITIONAL_max_mac.max_mac_MOD_0_0): + '${CONDITIONAL_max_mac.max_mac_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_max_mac.max_mac_MOD_1_0): + '${CONDITIONAL_max_mac.max_mac_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_maf_succ.CONDITIONAL_SELECT_maf_succ) == "set": + --maf-succ + + +#end if + +#if str($CONDITIONAL_min_alleles.CONDITIONAL_SELECT_min_alleles) == "set": + --min-alleles + + + #if $str($CONDITIONAL_min_alleles.min_alleles_MOD_0_0): + '${CONDITIONAL_min_alleles.min_alleles_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_max_alleles.CONDITIONAL_SELECT_max_alleles) == "set": + --max-alleles + + + #if $str($CONDITIONAL_max_alleles.max_alleles_MOD_0_0): + '${CONDITIONAL_max_alleles.max_alleles_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_read_freq.CONDITIONAL_SELECT_read_freq) == "set": + --read-freq + + + #if $str($CONDITIONAL_read_freq.read_freq_MOD_0_0): + '${CONDITIONAL_read_freq.read_freq_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_hwe.CONDITIONAL_SELECT_hwe) == "set": + --hwe + + + #if $str($CONDITIONAL_hwe.hwe_MOD_0_0): + '${CONDITIONAL_hwe.hwe_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_hwe.hwe_MOD_1_0): + '${CONDITIONAL_hwe.hwe_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_hwe.hwe_MOD_2_0): + '${CONDITIONAL_hwe.hwe_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_mach_r2_filter.CONDITIONAL_SELECT_mach_r2_filter) == "set": + --mach-r2-filter + + + #if $str($CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_0_0): + '${CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_1_0): + '${CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_minimac3_r2_filter.CONDITIONAL_SELECT_minimac3_r2_filter) == "set": + --minimac3-r2-filter + + + #if $str($CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_0_0): + '${CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_1_0): + '${CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_keep_females.CONDITIONAL_SELECT_keep_females) == "set": + --keep-females + + +#end if + +#if str($CONDITIONAL_keep_males.CONDITIONAL_SELECT_keep_males) == "set": + --keep-males + + +#end if + +#if str($CONDITIONAL_keep_nosex.CONDITIONAL_SELECT_keep_nosex) == "set": + --keep-nosex + + +#end if + +#if str($CONDITIONAL_remove_females.CONDITIONAL_SELECT_remove_females) == "set": + --remove-females + + +#end if + +#if str($CONDITIONAL_remove_males.CONDITIONAL_SELECT_remove_males) == "set": + --remove-males + + +#end if + +#if str($CONDITIONAL_remove_nosex.CONDITIONAL_SELECT_remove_nosex) == "set": + --remove-nosex + + +#end if + +#if str($CONDITIONAL_keep_founders.CONDITIONAL_SELECT_keep_founders) == "set": + --keep-founders + + +#end if + +#if str($CONDITIONAL_keep_nonfounders.CONDITIONAL_SELECT_keep_nonfounders) == "set": + --keep-nonfounders + + +#end if + +#if str($CONDITIONAL_keep_if.CONDITIONAL_SELECT_keep_if) == "set": + --keep-if + + + #if $str($CONDITIONAL_keep_if.keep_if_MOD_0_0): + '${CONDITIONAL_keep_if.keep_if_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_keep_if.keep_if_MOD_1_0): + '${CONDITIONAL_keep_if.keep_if_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_keep_if.keep_if_MOD_2_0): + '${CONDITIONAL_keep_if.keep_if_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_remove_if.CONDITIONAL_SELECT_remove_if) == "set": + --remove-if + + + #if $str($CONDITIONAL_remove_if.remove_if_MOD_0_0): + '${CONDITIONAL_remove_if.remove_if_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_remove_if.remove_if_MOD_1_0): + '${CONDITIONAL_remove_if.remove_if_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_remove_if.remove_if_MOD_2_0): + '${CONDITIONAL_remove_if.remove_if_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_nonfounders.CONDITIONAL_SELECT_nonfounders) == "set": + --nonfounders + + +#end if + +#if str($CONDITIONAL_bad_freqs.CONDITIONAL_SELECT_bad_freqs) == "set": + --bad-freqs + + +#end if + +#if str($CONDITIONAL_export_allele.CONDITIONAL_SELECT_export_allele) == "set": + --export-allele + + + #if $str($CONDITIONAL_export_allele.export_allele_MOD_0_0): + '${CONDITIONAL_export_allele.export_allele_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_output_chr.CONDITIONAL_SELECT_output_chr) == "set": + --output-chr + + + #if $str($CONDITIONAL_output_chr.output_chr_MOD_0_0): + '${CONDITIONAL_output_chr.output_chr_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_output_missing_genotype.CONDITIONAL_SELECT_output_missing_genotype) == "set": + --output-missing-genotype + + + #if $str($CONDITIONAL_output_missing_genotype.output_missing_genotype_MOD_0_0): + '${CONDITIONAL_output_missing_genotype.output_missing_genotype_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_output_missing_phenotype.CONDITIONAL_SELECT_output_missing_phenotype) == "set": + --output-missing-phenotype + + + #if $str($CONDITIONAL_output_missing_phenotype.output_missing_phenotype_MOD_0_0): + '${CONDITIONAL_output_missing_phenotype.output_missing_phenotype_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_sort_vars.CONDITIONAL_SELECT_sort_vars) == "set": + --sort-vars + + + #if $str($CONDITIONAL_sort_vars.sort_vars_MOD_0_0): + '${CONDITIONAL_sort_vars.sort_vars_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_set_hh_missing.CONDITIONAL_SELECT_set_hh_missing) == "set": + --set-hh-missing + + + #if $str($CONDITIONAL_set_hh_missing.set_hh_missing_MOD_0_0): + '${CONDITIONAL_set_hh_missing.set_hh_missing_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_set_mixed_mt_missing.CONDITIONAL_SELECT_set_mixed_mt_missing) == "set": + --set-mixed-mt-missing + + + #if $str($CONDITIONAL_set_mixed_mt_missing.set_mixed_mt_missing_MOD_0_0): + '${CONDITIONAL_set_mixed_mt_missing.set_mixed_mt_missing_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_OVERLOADED_SELECT_split_par) == "form_0": + #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.CONDITIONAL_SELECT_split_par) == "set": + --split-par + + #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0): + '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0): + '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_OVERLOADED_SELECT_split_par) == "form_1": + #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.CONDITIONAL_SELECT_split_par) == "set": + --split-par + + #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0): + '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0}' + #end if + #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0): + '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_merge_par.CONDITIONAL_SELECT_merge_par) == "set": + --merge-par + + +#end if + +#if str($CONDITIONAL_merge_x.CONDITIONAL_SELECT_merge_x) == "set": + --merge-x + + +#end if + +#if str($CONDITIONAL_set_missing_var_ids.CONDITIONAL_SELECT_set_missing_var_ids) == "set": + --set-missing-var-ids + + + #if $str($CONDITIONAL_set_missing_var_ids.set_missing_var_ids_MOD_0_0): + '${CONDITIONAL_set_missing_var_ids.set_missing_var_ids_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_set_all_var_ids.CONDITIONAL_SELECT_set_all_var_ids) == "set": + --set-all-var-ids + + + #if $str($CONDITIONAL_set_all_var_ids.set_all_var_ids_MOD_0_0): + '${CONDITIONAL_set_all_var_ids.set_all_var_ids_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_var_id_multi.CONDITIONAL_SELECT_var_id_multi) == "set": + --var-id-multi + + + #if $str($CONDITIONAL_var_id_multi.var_id_multi_MOD_0_0): + '${CONDITIONAL_var_id_multi.var_id_multi_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_var_id_multi_nonsnp.CONDITIONAL_SELECT_var_id_multi_nonsnp) == "set": + --var-id-multi-nonsnp + + + #if $str($CONDITIONAL_var_id_multi_nonsnp.var_id_multi_nonsnp_MOD_0_0): + '${CONDITIONAL_var_id_multi_nonsnp.var_id_multi_nonsnp_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_new_id_max_allele_len.CONDITIONAL_SELECT_new_id_max_allele_len) == "set": + --new-id-max-allele-len + + + #if $str($CONDITIONAL_new_id_max_allele_len.new_id_max_allele_len_MOD_0_0): + '${CONDITIONAL_new_id_max_allele_len.new_id_max_allele_len_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_new_id_max_allele_len.CONDITIONAL_new_id_max_allele_len_MOD_1.CONDITIONAL_SELECT_new_id_max_allele_len_MOD_1) == 'from_list' + '${CONDITIONAL_new_id_max_allele_len.CONDITIONAL_new_id_max_allele_len_MOD_1.new_id_max_allele_len_MOD_1}' + #end if + + +#end if + +#if str($CONDITIONAL_missing_var_code.CONDITIONAL_SELECT_missing_var_code) == "set": + --missing-var-code + + + #if $str($CONDITIONAL_missing_var_code.missing_var_code_MOD_0_0): + '${CONDITIONAL_missing_var_code.missing_var_code_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_update_map.CONDITIONAL_SELECT_update_map) == "set": + --update-map + + + #if $CONDITIONAL_update_map.update_map_MOD_0_0: + '${CONDITIONAL_update_map.update_map_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_update_map.update_map_MOD_1_0): + '${CONDITIONAL_update_map.update_map_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_update_map.update_map_MOD_2_0): + '${CONDITIONAL_update_map.update_map_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_update_map.update_map_MOD_3_0): + '${CONDITIONAL_update_map.update_map_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_update_name.CONDITIONAL_SELECT_update_name) == "set": + --update-name + + + #if $CONDITIONAL_update_name.update_name_MOD_0_0: + '${CONDITIONAL_update_name.update_name_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_update_name.update_name_MOD_1_0): + '${CONDITIONAL_update_name.update_name_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_update_name.update_name_MOD_2_0): + '${CONDITIONAL_update_name.update_name_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_update_name.update_name_MOD_3_0): + '${CONDITIONAL_update_name.update_name_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_recover_var_ids.CONDITIONAL_SELECT_recover_var_ids) == "set": + --recover-var-ids + + + #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_0_0): + '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_1_0): + '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_1_0}' + #end if + +#if $str($CONDITIONAL_recover_var_ids.CONDITIONAL_recover_var_ids_MOD_2.CONDITIONAL_SELECT_recover_var_ids_MOD_2) == 'from_list' + '${CONDITIONAL_recover_var_ids.CONDITIONAL_recover_var_ids_MOD_2.recover_var_ids_MOD_2}' + #end if + + + #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_3_0): + '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_update_alleles.CONDITIONAL_SELECT_update_alleles) == "set": + --update-alleles + + + #if $CONDITIONAL_update_alleles.update_alleles_MOD_0_0: + '${CONDITIONAL_update_alleles.update_alleles_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_update_ids.CONDITIONAL_SELECT_update_ids) == "set": + --update-ids + + + #if $CONDITIONAL_update_ids.update_ids_MOD_0_0: + '${CONDITIONAL_update_ids.update_ids_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_update_parents.CONDITIONAL_SELECT_update_parents) == "set": + --update-parents + + + #if $CONDITIONAL_update_parents.update_parents_MOD_0_0: + '${CONDITIONAL_update_parents.update_parents_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_update_sex.CONDITIONAL_SELECT_update_sex) == "set": + --update-sex + + + #if $CONDITIONAL_update_sex.update_sex_MOD_0_0: + '${CONDITIONAL_update_sex.update_sex_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_update_sex.update_sex_MOD_1_0): + '${CONDITIONAL_update_sex.update_sex_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_update_sex.update_sex_MOD_2_0): + '${CONDITIONAL_update_sex.update_sex_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_real_ref_alleles.CONDITIONAL_SELECT_real_ref_alleles) == "set": + --real-ref-alleles + + +#end if + +#if str($CONDITIONAL_maj_ref.CONDITIONAL_SELECT_maj_ref) == "set": + --maj-ref + + + #if $str($CONDITIONAL_maj_ref.maj_ref_MOD_0_0): + '${CONDITIONAL_maj_ref.maj_ref_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_ref_allele.CONDITIONAL_SELECT_ref_allele) == "set": + --ref-allele + + + #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_0_0): + '${CONDITIONAL_ref_allele.ref_allele_MOD_0_0}' + #end if + + #if $CONDITIONAL_ref_allele.ref_allele_MOD_1_0: + '${CONDITIONAL_ref_allele.ref_allele_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_2_0): + '${CONDITIONAL_ref_allele.ref_allele_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_3_0): + '${CONDITIONAL_ref_allele.ref_allele_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_4_0): + '${CONDITIONAL_ref_allele.ref_allele_MOD_4_0}' + #end if + +#end if + +#if str($CONDITIONAL_alt1_allele.CONDITIONAL_SELECT_alt1_allele) == "set": + --alt1-allele + + + #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_0_0): + '${CONDITIONAL_alt1_allele.alt1_allele_MOD_0_0}' + #end if + + #if $CONDITIONAL_alt1_allele.alt1_allele_MOD_1_0: + '${CONDITIONAL_alt1_allele.alt1_allele_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_2_0): + '${CONDITIONAL_alt1_allele.alt1_allele_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_3_0): + '${CONDITIONAL_alt1_allele.alt1_allele_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_4_0): + '${CONDITIONAL_alt1_allele.alt1_allele_MOD_4_0}' + #end if + +#end if + +#if str($CONDITIONAL_ref_from_fa.CONDITIONAL_SELECT_ref_from_fa) == "set": + --ref-from-fa + + + #if $str($CONDITIONAL_ref_from_fa.ref_from_fa_MOD_0_0): + '${CONDITIONAL_ref_from_fa.ref_from_fa_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_normalize.CONDITIONAL_SELECT_normalize) == "set": + --normalize + + + #if $str($CONDITIONAL_normalize.normalize_MOD_0_0): + '${CONDITIONAL_normalize.normalize_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_indiv_sort.CONDITIONAL_SELECT_indiv_sort) == "set": + --indiv-sort + + + #if $str($CONDITIONAL_indiv_sort.indiv_sort_MOD_0_0): + '${CONDITIONAL_indiv_sort.indiv_sort_MOD_0_0}' + #end if + + #if $CONDITIONAL_indiv_sort.indiv_sort_MOD_1_0: + '${CONDITIONAL_indiv_sort.indiv_sort_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_king_table_filter.CONDITIONAL_SELECT_king_table_filter) == "set": + --king-table-filter + + + #if $str($CONDITIONAL_king_table_filter.king_table_filter_MOD_0_0): + '${CONDITIONAL_king_table_filter.king_table_filter_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_king_table_subset.CONDITIONAL_SELECT_king_table_subset) == "set": + --king-table-subset + + + #if $CONDITIONAL_king_table_subset.king_table_subset_MOD_0_0: + '${CONDITIONAL_king_table_subset.king_table_subset_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_king_table_subset.king_table_subset_MOD_1_0): + '${CONDITIONAL_king_table_subset.king_table_subset_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_condition.CONDITIONAL_SELECT_condition) == "set": + --condition + + + #if $str($CONDITIONAL_condition.condition_MOD_0_0): + '${CONDITIONAL_condition.condition_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_condition.CONDITIONAL_condition_MOD_1.CONDITIONAL_SELECT_condition_MOD_1) == 'from_list' + '${CONDITIONAL_condition.CONDITIONAL_condition_MOD_1.condition_MOD_1}' + #end if + + + #if $str($CONDITIONAL_condition.condition_MOD_2_0): + '${CONDITIONAL_condition.condition_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_condition_list.CONDITIONAL_SELECT_condition_list) == "set": + --condition-list + + + #if $CONDITIONAL_condition_list.condition_list_MOD_0_0: + '${CONDITIONAL_condition_list.condition_list_MOD_0_0}' + #end if + +#if $str($CONDITIONAL_condition_list.CONDITIONAL_condition_list_MOD_1.CONDITIONAL_SELECT_condition_list_MOD_1) == 'from_list' + '${CONDITIONAL_condition_list.CONDITIONAL_condition_list_MOD_1.condition_list_MOD_1}' + #end if + + + #if $str($CONDITIONAL_condition_list.condition_list_MOD_2_0): + '${CONDITIONAL_condition_list.condition_list_MOD_2_0}' + #end if + +#end if + +#if str($CONDITIONAL_parameters.CONDITIONAL_SELECT_parameters) == "set": + --parameters + + + #if $str($CONDITIONAL_parameters.parameters_MOD_0_0): + '${CONDITIONAL_parameters.parameters_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_OVERLOADED_SELECT_tests) == "form_0": + #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.CONDITIONAL_SELECT_tests) == "set": + --tests + + #if $str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.tests_MOD_0_0): + '${CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.tests_MOD_0_0}' + #end if +#end if + #end if + +#if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_OVERLOADED_SELECT_tests) == "form_1": + #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.CONDITIONAL_SELECT_tests) == "set": + --tests + +#end if + #end if + +#if str($CONDITIONAL_vif.CONDITIONAL_SELECT_vif) == "set": + --vif + + + #if $str($CONDITIONAL_vif.vif_MOD_0_0): + '${CONDITIONAL_vif.vif_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_max_corr.CONDITIONAL_SELECT_max_corr) == "set": + --max-corr + + + #if $str($CONDITIONAL_max_corr.max_corr_MOD_0_0): + '${CONDITIONAL_max_corr.max_corr_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_xchr_model.CONDITIONAL_SELECT_xchr_model) == "set": + --xchr-model + + + #if $str($CONDITIONAL_xchr_model.xchr_model_MOD_0_0): + '${CONDITIONAL_xchr_model.xchr_model_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust.CONDITIONAL_SELECT_adjust) == "set": + --adjust + + + #if $str($CONDITIONAL_adjust.adjust_MOD_0_0): + '${CONDITIONAL_adjust.adjust_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_adjust.adjust_MOD_1_0): + '${CONDITIONAL_adjust.adjust_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_adjust.adjust_MOD_2_0): + '${CONDITIONAL_adjust.adjust_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_adjust.adjust_MOD_3_0): + '${CONDITIONAL_adjust.adjust_MOD_3_0}' + #end if + +#end if + +#if str($CONDITIONAL_lambda.CONDITIONAL_SELECT_lambda) == "set": + --lambda + + +#end if + +#if str($CONDITIONAL_adjust_chr_field.CONDITIONAL_SELECT_adjust_chr_field) == "set": + --adjust-chr-field + + + #if $str($CONDITIONAL_adjust_chr_field.adjust_chr_field_MOD_0_0): + '${CONDITIONAL_adjust_chr_field.adjust_chr_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_pos_field.CONDITIONAL_SELECT_adjust_pos_field) == "set": + --adjust-pos-field + + + #if $str($CONDITIONAL_adjust_pos_field.adjust_pos_field_MOD_0_0): + '${CONDITIONAL_adjust_pos_field.adjust_pos_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_id_field.CONDITIONAL_SELECT_adjust_id_field) == "set": + --adjust-id-field + + + #if $str($CONDITIONAL_adjust_id_field.adjust_id_field_MOD_0_0): + '${CONDITIONAL_adjust_id_field.adjust_id_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_ref_field.CONDITIONAL_SELECT_adjust_ref_field) == "set": + --adjust-ref-field + + + #if $str($CONDITIONAL_adjust_ref_field.adjust_ref_field_MOD_0_0): + '${CONDITIONAL_adjust_ref_field.adjust_ref_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_alt_field.CONDITIONAL_SELECT_adjust_alt_field) == "set": + --adjust-alt-field + + + #if $str($CONDITIONAL_adjust_alt_field.adjust_alt_field_MOD_0_0): + '${CONDITIONAL_adjust_alt_field.adjust_alt_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_a1_field.CONDITIONAL_SELECT_adjust_a1_field) == "set": + --adjust-a1-field + + + #if $str($CONDITIONAL_adjust_a1_field.adjust_a1_field_MOD_0_0): + '${CONDITIONAL_adjust_a1_field.adjust_a1_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_test_field.CONDITIONAL_SELECT_adjust_test_field) == "set": + --adjust-test-field + + + #if $str($CONDITIONAL_adjust_test_field.adjust_test_field_MOD_0_0): + '${CONDITIONAL_adjust_test_field.adjust_test_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_adjust_p_field.CONDITIONAL_SELECT_adjust_p_field) == "set": + --adjust-p-field + + + #if $str($CONDITIONAL_adjust_p_field.adjust_p_field_MOD_0_0): + '${CONDITIONAL_adjust_p_field.adjust_p_field_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_ci.CONDITIONAL_SELECT_ci) == "set": + --ci + + + #if $str($CONDITIONAL_ci.ci_MOD_0_0): + '${CONDITIONAL_ci.ci_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_pfilter.CONDITIONAL_SELECT_pfilter) == "set": + --pfilter + + + #if $str($CONDITIONAL_pfilter.pfilter_MOD_0_0): + '${CONDITIONAL_pfilter.pfilter_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_score_col_nums.CONDITIONAL_SELECT_score_col_nums) == "set": + --score-col-nums + + + #if $str($CONDITIONAL_score_col_nums.score_col_nums_MOD_0_0): + '${CONDITIONAL_score_col_nums.score_col_nums_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_q_score_range.CONDITIONAL_SELECT_q_score_range) == "set": + --q-score-range + + + #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_0_0): + '${CONDITIONAL_q_score_range.q_score_range_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_1_0): + '${CONDITIONAL_q_score_range.q_score_range_MOD_1_0}' + #end if + + #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_2_0): + '${CONDITIONAL_q_score_range.q_score_range_MOD_2_0}' + #end if + + #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_3_0): + '${CONDITIONAL_q_score_range.q_score_range_MOD_3_0}' + #end if + + #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_4_0): + '${CONDITIONAL_q_score_range.q_score_range_MOD_4_0}' + #end if + + #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_5_0): + '${CONDITIONAL_q_score_range.q_score_range_MOD_5_0}' + #end if + +#end if + +#if str($CONDITIONAL_vscore_col_nums.CONDITIONAL_SELECT_vscore_col_nums) == "set": + --vscore-col-nums + + + #if $str($CONDITIONAL_vscore_col_nums.vscore_col_nums_MOD_0_0): + '${CONDITIONAL_vscore_col_nums.vscore_col_nums_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_memory.CONDITIONAL_SELECT_memory) == "set": + --memory + + + #if $str($CONDITIONAL_memory.memory_MOD_0_0): + '${CONDITIONAL_memory.memory_MOD_0_0}' + #end if + + #if $str($CONDITIONAL_memory.memory_MOD_1_0): + '${CONDITIONAL_memory.memory_MOD_1_0}' + #end if + +#end if + +#if str($CONDITIONAL_threads.CONDITIONAL_SELECT_threads) == "set": + --threads + + + #if $str($CONDITIONAL_threads.threads_MOD_0_0): + '${CONDITIONAL_threads.threads_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_d.CONDITIONAL_SELECT_d) == "set": + --d + + + #if $str($CONDITIONAL_d.d_MOD_0_0): + '${CONDITIONAL_d.d_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_seed.CONDITIONAL_SELECT_seed) == "set": + --seed + + + #if $str($CONDITIONAL_seed.seed_MOD_0_0): + '${CONDITIONAL_seed.seed_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_output_min_p.CONDITIONAL_SELECT_output_min_p) == "set": + --output-min-p + + + #if $str($CONDITIONAL_output_min_p.output_min_p_MOD_0_0): + '${CONDITIONAL_output_min_p.output_min_p_MOD_0_0}' + #end if + +#end if + +#if str($CONDITIONAL_debug.CONDITIONAL_SELECT_debug) == "set": + --debug + + +#end if + +#if str($CONDITIONAL_randmem.CONDITIONAL_SELECT_randmem) == "set": + --randmem + + +#end if + +#if str($CONDITIONAL_warning_errcode.CONDITIONAL_SELECT_warning_errcode) == "set": + --warning-errcode + + +#end if + +#if str($CONDITIONAL_zst_level.CONDITIONAL_SELECT_zst_level) == "set": + --zst-level + + + #if $str($CONDITIONAL_zst_level.zst_level_MOD_0_0): + '${CONDITIONAL_zst_level.zst_level_MOD_0_0}' + #end if + +#end if + ]]></command> + <inputs> + <conditional name="CONDITIONAL_pfile"> + <param name="CONDITIONAL_SELECT_pfile" type="select" label="Set Pfile" help="Specify .pgen + .pvar[.zst] + .psam prefix. " argument="--pfile"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pfile_MOD_0_0" type="text" label="prefix" value="" optional="True" argument="prefix" help=""/> + <param name="pfile_MOD_1_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_pgen"> + <param name="CONDITIONAL_SELECT_pgen" type="select" label="Set Pgen" help="Specify full name of .pgen/.bed file. " argument="--pgen"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pgen_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_pvar"> + <param name="CONDITIONAL_SELECT_pvar" type="select" label="Set Pvar" help="Specify full name of .pvar/.bim file. " argument="--pvar"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pvar_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_psam"> + <param name="CONDITIONAL_SELECT_psam" type="select" label="Set Psam" help="Specify full name of .psam/.fam file. " argument="--psam"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="psam_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_bpfile"> + <param name="CONDITIONAL_SELECT_bpfile" type="select" label="Set Bpfile" help="Specify .pgen + .bim[.zst] + .fam prefix. " argument="--bpfile"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="bpfile_MOD_0_0" type="text" label="prefix" value="" optional="True" argument="prefix" help=""/> + <param name="bpfile_MOD_1_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_autoconv"> + <param name="CONDITIONAL_SELECT_keep_autoconv" type="select" label="Set Keep autoconv" help="When importing non-PLINK-binary data, don't delete autogenerated binary fileset at end of run. " argument="--keep-autoconv"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_no_fid"> + <param name="CONDITIONAL_SELECT_no_fid" type="select" label="Set No fid" help=".fam file does not contain column 1 (family ID). " argument="--no-fid"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_no_parents"> + <param name="CONDITIONAL_SELECT_no_parents" type="select" label="Set No parents" help=".fam file does not contain columns 3-4 (parents). " argument="--no-parents"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_no_sex"> + <param name="CONDITIONAL_SELECT_no_sex" type="select" label="Set No sex" help=".fam file does not contain column 5 (sex). " argument="--no-sex"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_vcf"> + <param name="CONDITIONAL_SELECT_vcf" type="select" label="Set Vcf" help="" argument="--vcf"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vcf_MOD_0_0" type="data" format="vcf" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="vcf_MOD_1_0" type="text" label="'dosage='<field>" value="" optional="False" argument="'dosage='<field>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_bcf"> + <param name="CONDITIONAL_SELECT_bcf" type="select" label="Set Bcf" help="Specify full name of .vcf{|.gz|.zst} or BCF2 file to import. * These can be used with --psam/--fam. * By default, dosage information is not imported. To import the GP field (must be VCFv4.3-style 0..1, one probability per possible genotype), add 'dosage=GP' (or 'dosage=GP-force', see below). To import Minimac3-style DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else for now) causes the named field to be interpreted as a Minimac3-style dosage. Note that, in the dosage=GP case, PLINK 2 collapses the probabilities down to dosages; you cannot use PLINK 2 to losslessly convert VCF FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2 now errors out when dosage=GP is used on a file with a FORMAT:DS header line and --import-dosage-certainty wasn't specified, since dosage=DS extracts the same information more quickly in this situation. You can suppress this error with 'dosage=GP-force'. In all of these cases, hardcalls are regenerated from scratch from the dosages. As a consequence, variants with no GT field can now be imported; they will be assumed to contain only diploid calls when HDS is also absent." argument="--bcf"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="bcf_MOD_0_0" type="data" format="bcf" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="bcf_MOD_1_0" type="text" label="'dosage='<field>" value="" optional="False" argument="'dosage='<field>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_bgen"> + <param name="CONDITIONAL_SELECT_bgen" type="select" label="Set Bgen" help="" argument="--bgen"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="bgen_MOD_0_0" type="data" format="plink.bgen" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="bgen_MOD_1_0" type="text" label="REF/ALT mode" value="" optional="False" argument="REF/ALT mode" help=""/> + <param name="bgen_MOD_2_0" type="text" label="'snpid-chr'" value="" optional="False" argument="'snpid-chr'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_gen"> + <param name="CONDITIONAL_SELECT_gen" type="select" label="Set Gen" help="" argument="--gen"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="gen_MOD_0_0" type="data" format="plink.gen" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="gen_MOD_1_0" type="text" label="REF/ALT mode" value="" optional="False" argument="REF/ALT mode" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_sample"> + <param name="CONDITIONAL_SELECT_sample" type="select" label="Set Sample" help="Specify an Oxford-format dataset to import. --data specifies a .gen[.zst] + .sample pair, while --bgen specifies a BGEN v1.1+ file. * If a BGEN v1.2+ file contains sample IDs, it may be imported without a companion .sample file. * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field instead of the usual chromosome field. * The following REF/ALT modes are supported: 'ref-first': The first allele for each variant is REF. 'ref-last': The last allele for each variant is REF. 'ref-unknown' (default): The last allele for each variant is treated as provisional-REF. This parameter will be required instead of optional in alpha 3." argument="--sample"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="sample_MOD_0_0" type="data" format="plink.sample" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_haps"> + <param name="CONDITIONAL_SELECT_haps" type="select" label="Set Haps" help="" argument="--haps"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="haps_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <conditional name="CONDITIONAL_haps_MOD_1"> + <param name="CONDITIONAL_SELECT_haps_MOD_1" type="select" label="How to set Haps"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="haps_MOD_1" type="select" label="Select value"> + <option value="{ref-first">{ref-first</option> +<option value="ref-last}">ref-last}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_legend"> + <param name="CONDITIONAL_SELECT_legend" type="select" label="Set Legend" help="Specify .haps [+ .legend] file(s) to import. * When --legend is specified, it's assumed that the --haps file doesn't contain header columns. * On chrX, the second male column may contain dummy '-' entries. (However, PLINK 2 currently cannot handle omitted male columns.) * If not used with --sample, new sample IDs are of the form 'per#/per#'." argument="--legend"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="legend_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="legend_MOD_1_0" type="text" label="chr code" value="" optional="True" argument="chr code" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_map"> + <param name="CONDITIONAL_SELECT_map" type="select" label="Set Map" help="Specify full name of .map file. " argument="--map"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="map_MOD_0_0" type="data" format="plink.map" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_import_dosage"> + <param name="CONDITIONAL_SELECT_import_dosage" type="select" label="Set Import dosage" help="Specify PLINK 1.x-style dosage file to import. * You must also specify a companion .psam/.fam file. * By default, PLINK assumes that the file contains a header line, which has 'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are normally zero, but can be changed with 'skip0', 'skip1', and 'skip2' respectively. FID/IID are normally assumed to be separate tokens, but if they're merged into a single token you can specify the delimiter with 'id-delim='.) If such a header line is not present, use the 'noheader' modifier; samples will then be assumed to appear in the same order as they do in the .psam/.fam file. * You may specify a companion .map file. If you do not, * 'single-chr=' can be used to specify that all variants are on the named chromosome. Otherwise, you can use 'chr-col-num=' to read chromosome codes from the given (1-based) column number. * 'pos-col-num=' causes bp coordinates to be read from the given column number. * The 'format=' modifier lets you specify the number of values used to represent each dosage. 'format=1' normally indicates a single 0..2 A1 expected count; 'dose1' modifies this to a 0..1 frequency. 'format=2' indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2. 'format=infer' (the default) infers the format from the number of columns in the first nonheader line." argument="--import-dosage"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="import_dosage_MOD_0_0" type="text" label="allele dosage file" value="" optional="True" argument="allele dosage file" help=""/> + <param name="import_dosage_MOD_1_0" type="text" label="'noheader'" value="" optional="False" argument="'noheader'" help=""/> + <param name="import_dosage_MOD_2_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/> + <param name="import_dosage_MOD_3_0" type="text" label="'skip0='<i>" value="" optional="False" argument="'skip0='<i>" help=""/> + <param name="import_dosage_MOD_4_0" type="text" label="'skip1='<j>" value="" optional="False" argument="'skip1='<j>" help=""/> + <param name="import_dosage_MOD_5_0" type="text" label="'skip2='<k>" value="" optional="False" argument="'skip2='<k>" help=""/> + <param name="import_dosage_MOD_6_0" type="text" label="'dose1'" value="" optional="False" argument="'dose1'" help=""/> + <param name="import_dosage_MOD_7_0" type="text" label="'format='<m>" value="" optional="False" argument="'format='<m>" help=""/> + <conditional name="CONDITIONAL_import_dosage_MOD_8"> + <param name="CONDITIONAL_SELECT_import_dosage_MOD_8" type="select" label="How to set Import dosage"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="import_dosage_MOD_8" type="select" label="Select value"> + <option value="{ref-first">{ref-first</option> +<option value="ref-last}">ref-last}</option> +</param> + </when> + </conditional> + <param name="import_dosage_MOD_9_0" type="text" label="'single-chr='<code>" value="" optional="False" argument="'single-chr='<code>" help=""/> + <param name="import_dosage_MOD_10_0" type="text" label="'chr-col-num='<#>" value="" optional="False" argument="'chr-col-num='<#>" help=""/> + <param name="import_dosage_MOD_11_0" type="text" label="'pos-col-num='<#>" value="" optional="False" argument="'pos-col-num='<#>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_dummy"> + <param name="CONDITIONAL_SELECT_dummy" type="select" label="Set Dummy" help="This generates a fake input dataset with the specified number of samples and SNPs. * By default, the missing dosage and phenotype frequencies are zero. These can be changed by providing 3rd and 4th numeric parameters. * By default, allele codes are As and Bs; this can be changed with the 'acgt', '1234', or '12' modifier. * By default, one binary phenotype is generated. 'pheno-ct=' can be used to change the number of phenotypes, and 'scalar-pheno' causes these phenotypes to be normally distributed scalars. * By default, all (nonmissing) dosages are in {0,1,2}. To make some of them take on decimal values, use 'dosage-freq='. (These dosages are affected by --hard-call-threshold and --dosage-erase-threshold.)" argument="--dummy"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="dummy_MOD_0_0" type="text" label="sample ct" value="" optional="True" argument="sample ct" help=""/> + <param name="dummy_MOD_1_0" type="text" label="SNP ct" value="" optional="True" argument="SNP ct" help=""/> + <param name="dummy_MOD_2_0" type="text" label="missing dosage freq" value="" optional="False" argument="missing dosage freq" help=""/> + <param name="dummy_MOD_3_0" type="text" label="missing pheno freq" value="" optional="False" argument="missing pheno freq" help=""/> + <conditional name="CONDITIONAL_dummy_MOD_4"> + <param name="CONDITIONAL_SELECT_dummy_MOD_4" type="select" label="How to set Dummy"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="dummy_MOD_4" type="select" label="Select value"> + <option value="{acgt">{acgt</option> +<option value="1234">1234</option> +<option value="12}">12}</option> +</param> + </when> + </conditional> + <param name="dummy_MOD_5_0" type="text" label="'pheno-ct='<count>" value="" optional="False" argument="'pheno-ct='<count>" help=""/> + <param name="dummy_MOD_6_0" type="text" label="'scalar-pheno'" value="" optional="False" argument="'scalar-pheno'" help=""/> + <param name="dummy_MOD_7_0" type="text" label="'dosage-freq='<rate>" value="" optional="False" argument="'dosage-freq='<rate>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_fa"> + <param name="CONDITIONAL_SELECT_fa" type="select" label="Set Fa" help="Specify full name of reference FASTA file. " argument="--fa"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="fa_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_rm_dup"> + <param name="CONDITIONAL_SELECT_rm_dup" type="select" label="Set Rm dup" help="Remove all but one instance of each duplicate-ID variant (ignoring the missing ID), and (with the 'list' modifier) write a list of duplicated IDs to <output prefix>.rmdup.list. The following modes of operation are supported: * 'error' (default) causes this to error out when there's a genotype data or other mismatch between the records. A list of affected IDs is written to <output prefix>.rmdup.mismatch. * 'retain-mismatch' causes all instances of a duplicate-ID variant to be retained when there's a genotype data or variant info mismatch; otherwise one instance is kept. The .rmdup.mismatch file is also written. * 'exclude-mismatch' removes all instances of duplicate-ID mismatched variants instead. * 'exclude-all' causes all instances of duplicate-ID variants to be removed, even when the actual records are identical. * 'force-first' causes only the first instance of duplicate-ID variants to be kept, under all circumstances." argument="--rm-dup"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="rm_dup_MOD_0_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/> + <param name="rm_dup_MOD_1_0" type="text" label="'list'" value="" optional="False" argument="'list'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_pgen"> + <param name="CONDITIONAL_SELECT_make_pgen" type="select" label="Set Make pgen" help="" argument="--make-pgen"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_pgen_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/> + <param name="make_pgen_MOD_1_0" type="text" label="'format='<code>" value="" optional="False" argument="'format='<code>" help=""/> + <param name="make_pgen_MOD_2_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/> + <param name="make_pgen_MOD_3_0" type="text" label="'erase-phase'" value="" optional="False" argument="'erase-phase'" help=""/> + <param name="make_pgen_MOD_4_0" type="text" label="'erase-dosage'" value="" optional="False" argument="'erase-dosage'" help=""/> + <param name="make_pgen_MOD_5_0" type="text" label="'pvar-cols='<col set descriptor>" value="" optional="False" argument="'pvar-cols='<col set descriptor>" help=""/> + <param name="make_pgen_MOD_6_0" type="text" label="'psam-cols='<col set descriptor>" value="" optional="False" argument="'psam-cols='<col set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_bpgen"> + <param name="CONDITIONAL_SELECT_make_bpgen" type="select" label="Set Make bpgen" help="" argument="--make-bpgen"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_bpgen_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/> + <param name="make_bpgen_MOD_1_0" type="text" label="'format='<code>" value="" optional="False" argument="'format='<code>" help=""/> + <param name="make_bpgen_MOD_2_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/> + <param name="make_bpgen_MOD_3_0" type="text" label="'erase-phase'" value="" optional="False" argument="'erase-phase'" help=""/> + <param name="make_bpgen_MOD_4_0" type="text" label="'erase-dosage'" value="" optional="False" argument="'erase-dosage'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_bed"> + <param name="CONDITIONAL_SELECT_make_bed" type="select" label="Set Make bed" help="Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] + .psam, --make-bpgen = .pgen + .bim[.zst] + .fam). * Unlike the automatic text-to-binary converters (which only heed chromosome filters), this supports all of PLINK's filtering flags. * The 'vzs' modifier causes the variant file (.pvar/.bim) to be Zstd-compressed. * The 'format' modifier requests an uncompressed fixed-variant-width .pgen file. (These do not directly support multiallelic variants.) The following format code is currently supported: 2: just like .bed, except with an extended (12-byte instead of 3-byte) header containing variant/sample counts, and rotated genotype codes (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing). * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage information from being written to the new .pgen. * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT. Supported optional .pvar column sets are: xheader: All ## header lines (yeah, this is technically not a column), except for possibly FILTER/INFO definitions when those column(s) have been removed. Without this, only the #CHROM header line is kept. maybequal: QUAL. Omitted if all remaining values are missing. qual: Force QUAL column to be written even when empty. maybefilter: FILTER. Omitted if all remaining values are missing. filter: Force FILTER column to be written even when empty. maybeinfo: INFO. Omitted if all remaining values are missing, or if INFO:PR is the only subfield. info: Force INFO column to be written. maybecm: Centimorgan coordinate. Omitted if all remaining values = 0. cm: Force CM column to be written even when empty. The default is xheader,maybequal,maybefilter,maybeinfo,maybecm. * Supported column sets for the .psam file are: maybefid: Family ID, '0' = missing. Omitted if all values missing. fid: Force FID column to be written even when empty. maybesid: Source ID, '0' = missing. Omitted if all values missing. sid: Force SID column to be written even when empty. maybeparents: Father and mother IIDs. Omitted if all values missing. parents: Force PAT and MAT columns to be written even when empty. sex: '1' = male, '2' = female, 'NA' = missing. pheno1: First active phenotype. If none, all column entries are set to the --output-missing-phenotype string. phenos: All active phenotypes, if any. (Can be combined with pheno1 to force at least one phenotype column to be written.) The default is maybefid,maybesid,maybeparents,sex,phenos." argument="--make-bed"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_bed_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/> + <param name="make_bed_MOD_1_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_just_pvar"> + <param name="CONDITIONAL_SELECT_make_just_pvar" type="select" label="Set Make just pvar" help="" argument="--make-just-pvar"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_just_pvar_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="make_just_pvar_MOD_1_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_just_psam"> + <param name="CONDITIONAL_SELECT_make_just_psam" type="select" label="Set Make just psam" help="" argument="--make-just-psam"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_just_psam_MOD_0_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_just_bim"> + <param name="CONDITIONAL_SELECT_make_just_bim" type="select" label="Set Make just bim" help="" argument="--make-just-bim"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_just_bim_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + </when> + </conditional> + <param name="make_just_fam" type="boolean" label="Make just fam" truevalue="--make-just-fam" falsevalue="" optional="true" argument="--make-just-fam" help="Variants of --make-pgen/--make-bed which only write a new variant or sample file. These don't always require an input genotype file. USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary genotype data and your sample/variant indexes if you use these commands improperly. If you have any doubt, stick with --make-[b]pgen/--make-bed." checked="False"/> + <conditional name="CONDITIONAL_export"> + <param name="CONDITIONAL_SELECT_export" type="select" label="Set Export" help="Create a new fileset with all filters applied. The following output formats are supported: (actually, only A, AD, A-transpose, bgen-1.x, ind-major-bed, haps, hapslegend, oxford, and vcf are implemented for now) * '23': 23andMe 4-column format. This can only be used on a single sample's data (--keep may be handy), and does not support multicharacter allele codes. * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R. If you need uncounted alleles to be named in the header line, add the 'include-alt' modifier. * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding. Also supports 'include-alt'. * 'A-transpose': Variant-major 0/1/2. * 'beagle': Unphased per-autosome .dat and .map files, readable by early BEAGLE versions. * 'beagle-nomap': Single .beagle.dat file. * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample identifiers are stored in the .bgen (with id-delim and id-paste settings applied), and default precision is 16-bit (use the 'bits' modifier to reduce this). * 'bimbam': Regular BIMBAM format. * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not support multiple chromosomes. * 'fastphase': Per-chromosome fastPHASE files, with .chr-<chr #>.phase.inp filename extensions. * 'fastphase-1chr': Single .phase.inp file. Does not support multiple chromosomes. * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All data must be biallelic and phased. When the 'bgz' modifier is present, the .haps file is block-gzipped. * 'HV': Per-chromosome Haploview files, with .chr-<chr #>{.ped,.info} filename extensions. * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support multiple chromosomes. * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam). * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile. * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile + --reference. * 'list': Single genotype-based list, up to 4 lines per variant. To omit nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier. * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a genotype-based list which omits the most common genotype for each variant. Also supports 'omit-nonmale-y'. * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier is present, the .gen file is block-gzipped. * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file. * 'compound-genotypes': Same as 'ped', except that the space between each pair of same-variant allele codes is removed. * 'structure': Structure-format. * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with --tfile. * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are present, they are automatically merged with chrX, with proper handling of chromosome codes and male ploidy. When the 'bgz' modifier is present, the VCF file is block-gzipped. The 'id-paste' modifier controls which .psam columns are used to construct sample IDs (choices are maybefid, fid, iid, maybesid, and sid; default is maybefid,iid,maybesid), while the 'id-delim' modifier sets the character between the ID pieces (default '_'). Dosages are not exported unless the 'vcf-dosage=' modifier is present. The following five dosage export modes are supported: 'GP': genotype posterior probabilities (v4.3 only). 'DS': Minimac3-style dosages, omitted for hardcalls. 'DS-force': Minimac3-style dosages, never omit. 'HDS': Minimac3-style phased dosages, omitted for hardcalls and unphased calls. Also includes 'DS' output. 'HDS-force': Always report DS and HDS. In addition, * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles to be coded as '2', while '01' maps alt1 -> 0 and ref -> 1. * The 'spaces' modifier makes the output space-delimited instead of tab-delimited, whenever both are permitted. * For biallelic formats where it's unspecified whether the reference/major allele should appear first or second, --export defaults to second for compatibility with PLINK 1.9. Use 'ref-first' to change this. (Note that this doesn't apply to the 'A', 'AD', and 'A-transpose' formats; use --export-allele to control which alleles are counted there.)" argument="--export"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="export_MOD_0_0" type="text" label="output format(s)..." value="" optional="True" argument="output format(s)..." help="Multiple values are allowed"/> + <conditional name="CONDITIONAL_export_MOD_1"> + <param name="CONDITIONAL_SELECT_export_MOD_1" type="select" label="How to set Export"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="export_MOD_1" type="select" label="Select value"> + <option value="{01">{01</option> +<option value="12}">12}</option> +</param> + </when> + </conditional> + <param name="export_MOD_2_0" type="text" label="'bgz'" value="" optional="False" argument="'bgz'" help=""/> + <param name="export_MOD_3_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/> + <param name="export_MOD_4_0" type="text" label="'id-paste='<column set descriptor>" value="" optional="False" argument="'id-paste='<column set descriptor>" help=""/> + <param name="export_MOD_5_0" type="text" label="'include-alt'" value="" optional="False" argument="'include-alt'" help=""/> + <param name="export_MOD_6_0" type="text" label="'omit-nonmale-y'" value="" optional="False" argument="'omit-nonmale-y'" help=""/> + <param name="export_MOD_7_0" type="text" label="'spaces'" value="" optional="False" argument="'spaces'" help=""/> + <param name="export_MOD_8_0" type="text" label="'vcf-dosage='<field>" value="" optional="False" argument="'vcf-dosage='<field>" help=""/> + <param name="export_MOD_9_0" type="text" label="'ref-first'" value="" optional="False" argument="'ref-first'" help=""/> + <param name="export_MOD_10_0" type="text" label="'bits='<#>" value="" optional="False" argument="'bits='<#>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_freq"> + <param name="CONDITIONAL_SELECT_freq" type="select" label="Set Freq" help="['refbins='<comma-separated bin boundaries> | 'refbins-file='<file>] ['alt1bins='<comma-separated bin boundaries> | 'alt1bins-file='<file>] Empirical allele frequency report. By default, only founders are considered. Dosages are taken into account (e.g. heterozygous haploid calls count as 0.5). Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. reffreq: Reference allele frequency/dosage. alt1freq: Alt1 frequency/dosage. altfreq: Comma-separated frequencies/dosages for all alternate alleles. freq: Similar to altfreq, except ref is also included at the start. eq: Comma-separated <allele>=<freq> for all present alleles. (If no alleles are present, the column contains a single '.'.) eqz: Same as eq, except zero-counts are included. alteq/alteqz: Same as eq/eqz, except reference allele is omitted. numeq: 0=<freq>,1=<freq>, etc. Zero-counts are omitted. altnumeq: Same as numeq, except reference allele is omitted. machr2: Unphased MaCH imputation quality metric. minimac3r2: Phased Minimac3 imputation quality. nobs: Number of allele observations. The default is chrom,ref,alt,altfreq,nobs. Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with 'counts') file(s) are generated when 'refbins='/'refbins-file=' or 'alt1bins='/'alt1bins-file=' is present; these report the total number of frequencies or counts in each left-closed, right-open interval. (If you only want these histogram(s), and not the main report, add 'bins-only'.)" argument="--freq"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="freq_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="freq_MOD_1_0" type="text" label="'counts'" value="" optional="False" argument="'counts'" help=""/> + <param name="freq_MOD_2_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + <param name="freq_MOD_3_0" type="text" label="'bins-only'" value="" optional="False" argument="'bins-only'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_geno_counts"> + <param name="CONDITIONAL_SELECT_geno_counts" type="select" label="Set Geno counts" help="Variant-based hardcall genotype count report (considering both alleles simultaneously in the diploid case). Nonfounders are now included; use --keep-founders if this is a problem. Heterozygous haploid calls are treated as missing. Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. homref: Homozygous-ref count. refalt1: Heterozygous ref-alt1 count. refalt: Comma-separated het ref-altx counts. homalt1: Homozygous-alt1 count. altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-... order. xy: Similar to altxy, except the reference allele is treated as alt0, and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-... hapref: Haploid-ref count. hapalt1: Haploid-alt1 count. hapalt: Comma-separated haploid-altx counts. hap: Similar to hapalts, except ref is also included at the start. numeq: 0/0=<hom ref ct>,0/1=<het ref-alt1>,1/1=<hom alt1>,...,0=<hap ref> etc. Zero-counts are omitted. (If all genotypes are missing, the column contains a single '.'.) missing: Number of missing genotypes. nobs: Number of (nonmissing) genotype observations. The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing." argument="--geno-counts"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="geno_counts_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="geno_counts_MOD_1_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_sample_counts"> + <param name="CONDITIONAL_SELECT_sample_counts" type="select" label="Set Sample counts" help="Sample-based hardcall genotype count report. * Unknown-sex samples are treated as female. * Heterozygous haploid calls (MT included) are treated as missing. * As with other PLINK 2 commands, SNPs that have not been left-normalized are counted as non-SNP non-symbolic. (Use e.g. --normalize when that's a problem.) * Supported column sets are: maybefid: FID, if that column was present in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was present in the input. sid: Force SID column to be written even when absent in the input. sex: '1' = male, '2' = female, 'NA' = missing. hom: Homozygous genotype count. homref: Homozygous-ref genotype count. homalt: Homozygous-alt genotype count. homaltsnp: Homozygous-alt SNP count. het: Heterozygous genotype count. refalt: Heterozygous ref-altx genotype count. het2alt: Heterozygous altx-alty genotype count. hetsnp: Heterozygous SNP count. dipts: Diploid SNP transition count. ts: SNP transition count (excluding chrY for females). diptv: Diploid SNP transversion count. tv: SNP transversion count. dipnonsnpsymb: Diploid non-SNP, non-symbolic count. nonsnpsymb: Non-SNP, non-symbolic count. symbolic: Symbolic variant count. nonsnp: Non-SNP count. dipsingle: Number of singletons relative to this dataset, across just diploid calls. (Note that if the ALT allele in a chrX biallelic variant appears in exactly one female and one male, that counts as a singleton for just the female.) single: Number of singletons relative to this dataset. haprefwfemaley: Haploid-ref count, counting chrY for everyone. hapref: Haploid-ref count, excluding chrY for females. hapaltwfemaley: Haploid-alt count, counting chrY for everyone. hapalt: Haploid-alt count, excluding chrY for females. missingwfemaley: Missing call count, counting chrY for everyone. missing: Missing call count, excluding chrY for females. The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv, dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley. * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb', 'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous altx-alty call separately, since they can be of different subtypes. (I.e. if they are of the same subtype, the corresponding count is incremented by 2.) As a consequence, these columns are unaffected by variant split/join." argument="--sample-counts"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="sample_counts_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="sample_counts_MOD_1_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_missing"> + <param name="CONDITIONAL_SELECT_missing" type="select" label="Set Missing" help="Generate sample- and variant-based missing data reports (or just one report if 'sample-only'/'variant-only' is specified). As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats. Supported column sets in the sample-based report are: maybefid: FID, if that column was present in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was present in the input. sid: Force SID column to be written even when absent in the input. misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no phenotypes are loaded. missphenos: A Y/N column for each loaded phenotype. (Can be combined with misspheno1 to force at least one such column.) nmissdosage: Number of missing dosages. nmiss: Number of missing hardcalls, not counting het haploids. nmisshh: Number of missing hardcalls, counting het haploids. hethap: Number of heterozygous haploid hardcalls. nobs: Denominator (male count on chrY, otherwise total sample count). fmissdosage: Missing dosage rate. fmiss: Missing hardcall rate, not counting het haploids. fmisshh: Missing hardcall rate, counting het haploids. The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss. Supported column sets in the variant-based report are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. nmissdosage: Number of missing dosages. nmiss: Number of missing hardcalls, not counting het haploids. nmisshh: Number of missing hardcalls, counting het haploids. hethap: Number of heterozygous haploid calls. nobs: Number of potentially valid calls. fmissdosage: Missing dosage rate. fmiss: Missing hardcall rate, not counting het haploids. fmisshh: Missing hardcall rate, counting het haploids. fhethap: Heterozygous haploid rate. The default is chrom,nmiss,nobs,fmiss." argument="--missing"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="missing_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <conditional name="CONDITIONAL_missing_MOD_1"> + <param name="CONDITIONAL_SELECT_missing_MOD_1" type="select" label="How to set Missing"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="missing_MOD_1" type="select" label="Select value"> + <option value="{sample-only">{sample-only</option> +<option value="variant-only}">variant-only}</option> +</param> + </when> + </conditional> + <param name="missing_MOD_2_0" type="text" label="'scols='<column set descriptor>" value="" optional="False" argument="'scols='<column set descriptor>" help=""/> + <param name="missing_MOD_3_0" type="text" label="'vcols='<column set descriptor>" value="" optional="False" argument="'vcols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_hardy"> + <param name="CONDITIONAL_SELECT_hardy" type="select" label="Set Hardy" help="Hardy-Weinberg exact test p-value report(s). * By default, only founders are considered; change this with --nonfounders. * chrX is now omitted from the main <output prefix>.hardy report. Instead, (if present) it gets its own <output prefix>.hardy.x report based on the method described in Graffelman J, Weir BS (2016) Hardy-Weinberg equilibrium and the X chromosome. * For variants with k alleles where k>2, k separate 'biallelic' tests are performed, each reported on its own line. However, biallelic variants are normally reported on a single line, since the counts/frequencies would be mirror-images and the p-values would be the same. You can add the 'redundant' modifier to force biallelic variant results to be reported on two lines for parsing convenience. * There is currently no special handling of case/control phenotypes. Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. (A1 is always present, and positioned here.) ax: Non-A1 allele(s), comma-separated. gcounts: Hom-A1 count, total number of het-A1 calls, and total number of nonmissing calls with no copies of A1. On chrX, these are followed by male A1 and male non-A1 counts. gcount1col: gcounts values in a single comma-separated column. hetfreq: Observed and expected het-A1 frequencies. sexaf: Female and male A1 observed allele frequencies (chrX only). femalep: Female-only p/midp-value (chrX only). p: Hardy-Weinberg equilibrium exact test p/midp-value. The default is chrom,ax,gcounts,hetfreq,sexaf,p." argument="--hardy"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="hardy_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="hardy_MOD_1_0" type="text" label="'midp'" value="" optional="False" argument="'midp'" help=""/> + <param name="hardy_MOD_2_0" type="text" label="'redundant'" value="" optional="False" argument="'redundant'" help=""/> + <param name="hardy_MOD_3_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_indep_pairwise"> + <param name="CONDITIONAL_SELECT_indep_pairwise" type="select" label="Set Indep pairwise" help="Generate a list of variants in approximate linkage equilibrium. * For multiallelic variants, major allele counts are used in the r^2 computation. * With the 'kb' modifier, the window size is in kilobase instead of variant count units. (Pre-'kb' space is optional, i.e. "--indep-pairwise 500 kb 0.5" and "--indep-pairwise 500kb 0.5" have the same effect.) * The step size now defaults to 1 if it's unspecified, and *must* be 1 if the window is in kilobase units. * Note that you need to rerun PLINK using --extract or --exclude on the .prune.in/.prune.out file to apply the list to another computation... and as with other applications of --extract/--exclude, duplicate variant IDs are a problem. --indep-pairwise still runs to completion for now when duplicate variant IDs are present, but that will become an error in alpha 3." argument="--indep-pairwise"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="indep_pairwise_MOD_0_0" type="text" label="window size" value="" optional="True" argument="window size" help=""/> + <param name="indep_pairwise_MOD_1_0" type="text" label="'kb'" value="" optional="False" argument="'kb'" help=""/> + <param name="indep_pairwise_MOD_2_0" type="text" label="step size (variant ct)" value="" optional="False" argument="step size (variant ct)" help=""/> + <param name="indep_pairwise_MOD_3_0" type="text" label="unphased-hardcall-r^2 threshold" value="" optional="True" argument="unphased-hardcall-r^2 threshold" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_ld"> + <param name="CONDITIONAL_SELECT_ld" type="select" label="Set Ld" help="This displays diplotype frequencies, r^2, and D' for a single pair of variants. * For multiallelic variants, major allele counts/dosages are used. * Phase information is used when both variants are on the same chromosome. * When there is at least one sample with unphased het calls for both variants, diplotype frequencies are estimated using the Hill equation. If there are multiple biologically possible local maxima, all are displayed, along with HWE exact test statistics. * By default, only hardcalls are considered. Add the 'dosage' modifier if you want dosages to be taken into account. (In the diploid case, an unphased dosage of x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x is in 0..1.)" argument="--ld"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="ld_MOD_0_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/> + <param name="ld_MOD_1_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/> + <param name="ld_MOD_2_0" type="text" label="'dosage'" value="" optional="False" argument="'dosage'" help=""/> + <param name="ld_MOD_3_0" type="text" label="'hwe-midp'" value="" optional="False" argument="'hwe-midp'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_OVERLOADED_sample_diff"> + <param name="CONDITIONAL_OVERLOADED_SELECT_sample_diff" type="select" label="Choose argument form for Sample_diff" help="Overloaded argument, must chose a form"> + <option value="form_0">Form 0</option> + <option value="form_1">Form 1</option> + </param> + <when value="form_0"> + + <conditional name="CONDITIONAL_sample_diff"> + <param name="CONDITIONAL_SELECT_sample_diff" type="select" label="Set Sample diff" help="" argument="--sample-diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="sample_diff_MOD_0_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/> + <conditional name="CONDITIONAL_sample_diff_MOD_1"> + <param name="CONDITIONAL_SELECT_sample_diff_MOD_1" type="select" label="How to set Sample diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="sample_diff_MOD_1" type="select" label="Select value"> + <option value="'dosage'">'dosage'</option> +<option value="'dosage='<tolerance>">'dosage='<tolerance></option> +</param> + </when> + </conditional> + <param name="sample_diff_MOD_2_0" type="text" label="'include-missing'" value="" optional="False" argument="'include-missing'" help=""/> + <conditional name="CONDITIONAL_sample_diff_MOD_3"> + <param name="CONDITIONAL_SELECT_sample_diff_MOD_3" type="select" label="How to set Sample diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="sample_diff_MOD_3" type="select" label="Select value"> + <option value="{pairwise">{pairwise</option> +<option value="counts-only}">counts-only}</option> +</param> + </when> + </conditional> + <param name="sample_diff_MOD_4_0" type="text" label="'fname-id-delim='<c>" value="" optional="False" argument="'fname-id-delim='<c>" help=""/> + <param name="sample_diff_MOD_5_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="sample_diff_MOD_6_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + <param name="sample_diff_MOD_7_0" type="text" label="'counts-cols='<column set descriptor>" value="" optional="False" argument="'counts-cols='<column set descriptor>" help=""/> + <conditional name="CONDITIONAL_sample_diff_MOD_8"> + <param name="CONDITIONAL_SELECT_sample_diff_MOD_8" type="select" label="How to set Sample diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="sample_diff_MOD_8" type="select" label="Select value"> + <option value="base=">base=</option> +<option value="ids=">ids=</option> +</param> + </when> + </conditional> + <param name="sample_diff_MOD_9_0" type="text" label="sample ID" value="" optional="True" argument="sample ID" help=""/> + <param name="sample_diff_MOD_10_0" type="text" label="other sample ID(s)..." value="" optional="False" argument="other sample ID(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + </when> + <when value="form_1"> + + <conditional name="CONDITIONAL_sample_diff"> + <param name="CONDITIONAL_SELECT_sample_diff" type="select" label="Set Sample diff" help="(alias: --sdiff) Report discordances and discordance-counts between pairs of samples. If chrX or chrY is present, sex must be defined and consistent. * There are three ways to specify which sample pairs to compare. To compare a single baseline sample against some others, start the (space-delimited) sample ID list with 'base='. To perform an all-vs.-all comparison, start it with 'ids=' instead. To compare sample pairs listed in a file, use 'file='. Note that 'base='/'ids='/'file=' must be positioned after all modifiers. * Sample IDs are interpreted as if they were in a VCF header line, with 'id-delim=' having the usual effect. * By default, comparisons are based on hardcalls. Use 'dosage' to compare dosages instead; you can combine this with a tolerance in [0, 0.5). * By default, if one genotype is missing and the other isn't, that doesn't count as a difference; this can be changed with 'include-missing'. * By default, a single main report is written to <output prefix>[.<base ID>].sdiff. To write separate pairwise <output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add the 'pairwise' modifier. To omit the main report, add the 'counts-only' modifier. (Note that, if you're only interested in nonmissing autosomal biallelic hardcalls, --make-king-table provides a more efficient way to compute just counts.) * By default, if an output filename has a multipart sample ID, the parts will be delimited by '_'; use 'fname-id-delim=' to change this. Supported main-report column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (Variant ID is always present, and positioned here.) ref: Reference allele. alt: All alternate alleles, comma-separated. maybefid: FID1/FID2, if that column was in the input. Requires 'id'. fid: Force FID1/FID2 even when FID was absent in the input. id: IID1/IID2. maybesid: SID1/SID2, if that column was in the input. Requires 'id'. sid: Force SID1/SID2 even when SID was absent in the input. geno: Unphased GT or DS for the two samples. The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the sample IDs are removed from the default in 'pairwise' mode. Supported discordance-count-summary column sets are: maybefid: FID1/FID2, if that column was in the input. fid: Force FID1/FID2 even when FID was absent in the input. (IID1/IID2 are always present.) maybesid: SID1/SID2, if that column was in the input. sid: Force SID1/SID2 even when SID was absent in the input. nobs: Number of variants considered. This includes variants where one or both variants are missing iff 'include-missing' was specified. nobsibs: ibs0+ibs1+ibs2. ibs0: Number of diploid variants with no common hardcall alleles. ibs1: Number of diploid variants with exactly 1 common hardcall allele. ibs2: Number of diploid variants with both hardcall alleles matching. halfmiss: Number of variants with exactly 1 missing genotype/dosage. Ignored without 'include-missing'. diff: Total number of differences. The default is maybefid,maybesid,nobs,halfmiss,diff." argument="--sample-diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="sample_diff_MOD_0_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/> + <conditional name="CONDITIONAL_sample_diff_MOD_1"> + <param name="CONDITIONAL_SELECT_sample_diff_MOD_1" type="select" label="How to set Sample diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="sample_diff_MOD_1" type="select" label="Select value"> + <option value="'dosage'">'dosage'</option> +<option value="'dosage='<tolerance>">'dosage='<tolerance></option> +</param> + </when> + </conditional> + <param name="sample_diff_MOD_2_0" type="text" label="'include-missing'" value="" optional="False" argument="'include-missing'" help=""/> + <conditional name="CONDITIONAL_sample_diff_MOD_3"> + <param name="CONDITIONAL_SELECT_sample_diff_MOD_3" type="select" label="How to set Sample diff"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="sample_diff_MOD_3" type="select" label="Select value"> + <option value="{pairwise">{pairwise</option> +<option value="counts-only}">counts-only}</option> +</param> + </when> + </conditional> + <param name="sample_diff_MOD_4_0" type="text" label="'fname-id-delim='<c>" value="" optional="False" argument="'fname-id-delim='<c>" help=""/> + <param name="sample_diff_MOD_5_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="sample_diff_MOD_6_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + <param name="sample_diff_MOD_7_0" type="text" label="'counts-cols='<column set descriptor>" value="" optional="False" argument="'counts-cols='<column set descriptor>" help=""/> + <param name="sample_diff_MOD_8_0" type="text" label="ID-pair file" value="" optional="True" argument="ID-pair file" help=""/> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_make_king"> + <param name="CONDITIONAL_SELECT_make_king" type="select" label="Set Make king" help="KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in genome-wide association studies. By default, this writes a lower-triangular tab-delimited table of kinship coefficients to <output prefix>.king, and a list of the corresponding sample IDs to <output prefix>.king.id. The first row of the .king file contains a single <genome 1-genome 2> kinship coefficient, the second row has the <genome 1-genome 3> and <genome 2-genome 3> kinship values in that order, etc. * Only autosomes are currently considered. * Pedigree information is currently ignored; the between-family estimator is used for all pairs. * For multiallelic variants, REF allele counts are used. * If the 'square' or 'square0' modifier is present, a square matrix is written instead; 'square0' fills the upper right triangle with zeroes. * If the 'zs' modifier is present, the .king file is Zstd-compressed. * If the 'bin' modifier is present, a binary (square) matrix of double-precision floating point values, suitable for loading from R, is instead written to <output prefix>.king.bin. ('bin4' specifies single-precision numbers instead.) This can be combined with 'square0' if you still want the upper right zeroed out, or 'triangle' if you don't want to pad the upper right at all. * The computation can be subdivided with --parallel." argument="--make-king"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <conditional name="CONDITIONAL_make_king_MOD_0"> + <param name="CONDITIONAL_SELECT_make_king_MOD_0" type="select" label="How to set Make king"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="make_king_MOD_0" type="select" label="Select value"> + <option value="{square">{square</option> +<option value="square0">square0</option> +<option value="triangle}">triangle}</option> +</param> + </when> + </conditional> + <conditional name="CONDITIONAL_make_king_MOD_1"> + <param name="CONDITIONAL_SELECT_make_king_MOD_1" type="select" label="How to set Make king"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="make_king_MOD_1" type="select" label="Select value"> + <option value="{zs">{zs</option> +<option value="bin">bin</option> +<option value="bin4}">bin4}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_make_king_table"> + <param name="CONDITIONAL_SELECT_make_king_table" type="select" label="Set Make king table" help="Similar to --make-king, except results are reported in KING's original .kin0 text table format (with minor changes, e.g. row order is more friendly to incremental addition of samples), --king-table-filter can be used to restrict the report to high kinship values, and the 'rel-check' modifier can be used to restrict to same-FID pairs. Supported column sets are: maybefid: FID1/FID2, if that column was in the input. Requires 'id'. fid: Force FID1/FID2 even when FID was absent in the input. id: IID1/IID2 (column headers are actually 'ID1'/'ID2' to match KING). maybesid: SID1/SID2, if that column was in the input. Requires 'id'. sid: Force SID1/SID2 even when SID was absent in the input. nsnp: Number of variants considered (autosomal, neither call missing). hethet: Proportion/count of considered call pairs which are het-het. ibs0: Proportion/count of considered call pairs which are opposite homs. ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts. kinship: KING-robust between-family kinship estimator. The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship. hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is present. If id is omitted, a .kin0.id file is also written." argument="--make-king-table"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_king_table_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="make_king_table_MOD_1_0" type="text" label="'counts'" value="" optional="False" argument="'counts'" help=""/> + <param name="make_king_table_MOD_2_0" type="text" label="'rel-check'" value="" optional="False" argument="'rel-check'" help=""/> + <param name="make_king_table_MOD_3_0" type="text" label="'cols='<col set descrip.>" value="" optional="False" argument="'cols='<col set descrip.>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_make_rel"> + <param name="CONDITIONAL_SELECT_make_rel" type="select" label="Set Make rel" help="Write a lower-triangular variance-standardized relationship matrix to <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id. * This computation assumes that variants do not have very low MAF, or deviate greatly from Hardy-Weinberg equilibrium. * Also, it's usually best to perform this calculation on a variant set in approximate linkage equilibrium. * The 'cov' modifier replaces the variance-standardization step with basic mean-centering, causing a covariance matrix to be calculated instead. * The computation can be subdivided with --parallel." argument="--make-rel"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_rel_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/> + <param name="make_rel_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/> + <conditional name="CONDITIONAL_make_rel_MOD_2"> + <param name="CONDITIONAL_SELECT_make_rel_MOD_2" type="select" label="How to set Make rel"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="make_rel_MOD_2" type="select" label="Select value"> + <option value="{square">{square</option> +<option value="square0">square0</option> +<option value="triangle}">triangle}</option> +</param> + </when> + </conditional> + <conditional name="CONDITIONAL_make_rel_MOD_3"> + <param name="CONDITIONAL_SELECT_make_rel_MOD_3" type="select" label="How to set Make rel"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="make_rel_MOD_3" type="select" label="Select value"> + <option value="{zs">{zs</option> +<option value="bin">bin</option> +<option value="bin4}">bin4}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_make_grm_list"> + <param name="CONDITIONAL_SELECT_make_grm_list" type="select" label="Set Make grm list" help="" argument="--make-grm-list"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_grm_list_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/> + <param name="make_grm_list_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/> + <param name="make_grm_list_MOD_2_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <conditional name="CONDITIONAL_make_grm_list_MOD_3"> + <param name="CONDITIONAL_SELECT_make_grm_list_MOD_3" type="select" label="How to set Make grm list"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="make_grm_list_MOD_3" type="select" label="Select value"> + <option value="{id-header">{id-header</option> +<option value="iid-only}">iid-only}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_make_grm_bin"> + <param name="CONDITIONAL_SELECT_make_grm_bin" type="select" label="Set Make grm bin" help="--make-grm-list causes the relationships to be written to GCTA's original list format, which describes one pair per line, while --make-grm-bin writes them in GCTA 1.1+'s single-precision triangular binary format. Note that these formats explicitly report the number of valid observations (where neither sample has a missing call) for each pair, which is useful input for some scripts." argument="--make-grm-bin"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="make_grm_bin_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/> + <param name="make_grm_bin_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/> + <conditional name="CONDITIONAL_make_grm_bin_MOD_2"> + <param name="CONDITIONAL_SELECT_make_grm_bin_MOD_2" type="select" label="How to set Make grm bin"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="make_grm_bin_MOD_2" type="select" label="Select value"> + <option value="{id-header">{id-header</option> +<option value="iid-only}">iid-only}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_OVERLOADED_pca"> + <param name="CONDITIONAL_OVERLOADED_SELECT_pca" type="select" label="Choose argument form for Pca" help="Overloaded argument, must chose a form"> + <option value="form_0">Form 0</option> + <option value="form_1">Form 1</option> + </param> + <when value="form_0"> + + <conditional name="CONDITIONAL_pca"> + <param name="CONDITIONAL_SELECT_pca" type="select" label="Set Pca" help="" argument="--pca"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pca_MOD_0_0" type="text" label="count" value="" optional="False" argument="count" help=""/> + <conditional name="CONDITIONAL_pca_MOD_1"> + <param name="CONDITIONAL_SELECT_pca_MOD_1" type="select" label="How to set Pca"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="pca_MOD_1" type="select" label="Select value"> + <option value="{approx">{approx</option> +<option value="meanimpute}">meanimpute}</option> +</param> + </when> + </conditional> + <param name="pca_MOD_2_0" type="text" label="'scols='<col set descriptor>" value="" optional="False" argument="'scols='<col set descriptor>" help=""/> + </when> + </conditional> + </when> + <when value="form_1"> + + <conditional name="CONDITIONAL_pca"> + <param name="CONDITIONAL_SELECT_pca" type="select" label="Set Pca" help="['scols='<col set descriptor>] ['vcols='<col set descriptor>] Extracts top principal components from the variance-standardized relationship matrix. * It is usually best to perform this calculation on a variant set in approximate linkage equilibrium, with no very-low-MAF variants. * By default, 10 PCs are extracted; you can adjust this by passing a numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of 20; this is due to the randomized algorithm's memory footprint growing quadratically w.r.t. the PC count.) * The 'approx' modifier causes the standard deterministic computation to be replaced with the randomized algorithm originally implemented for Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL (2016) Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. This can be a good idea when you have >5k samples. * The randomized algorithm always uses mean imputation for missing genotype calls. For comparison purposes, you can use the 'meanimpute' modifier to request this behavior for the standard computation. * 'scols=' can be used to customize how sample IDs appear in the .eigenvec file. (maybefid, fid, maybesid, and sid supported; default is maybefid,maybesid.) * The 'biallelic-var-wts' modifier requests an additional one-line-per-variant .eigenvec.var file with PCs expressed as variant weights instead of sample weights, with the condition that all variants must be biallelic. When it's present, 'vzs' causes the .eigenvec.var file to be Zstd-compressed. 'vcols=' can be used to customize the report columns; supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. maj: Major allele. nonmaj: All nonmajor alleles, comma-separated. (PCs are always present, and positioned here. Signs are w.r.t. the major, not necessarily reference, allele.) Default is chrom,maj,nonmaj. * In this build, 'var-wts' generates the same report as biallelic-var-wts, except with the "all variants must be biallelic" restriction lifted. This is temporary. It will no longer be supported as of alpha 3; instead, there will be an 'allele-wts' mode which seamlessly handles multiallelic variants, at the cost of generating more verbose one-line-per-allele output." argument="--pca"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <conditional name="CONDITIONAL_pca_MOD_0"> + <param name="CONDITIONAL_SELECT_pca_MOD_0" type="select" label="How to set Pca"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="pca_MOD_0" type="select" label="Select value"> + <option value="{biallelic-var-wts">{biallelic-var-wts</option> +<option value="var-wts}">var-wts}</option> +</param> + </when> + </conditional> + <param name="pca_MOD_1_0" type="text" label="count" value="" optional="False" argument="count" help=""/> + <conditional name="CONDITIONAL_pca_MOD_2"> + <param name="CONDITIONAL_SELECT_pca_MOD_2" type="select" label="How to set Pca"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="pca_MOD_2" type="select" label="Select value"> + <option value="{approx">{approx</option> +<option value="meanimpute}">meanimpute}</option> +</param> + </when> + </conditional> + <param name="pca_MOD_3_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_king_cutoff"> + <param name="CONDITIONAL_SELECT_king_cutoff" type="select" label="Set King cutoff" help="Exclude one member of each pair of samples with KING-robust kinship greater than the given threshold. Remaining/excluded sample IDs are written to <output prefix>.king.cutoff.in.id + .king.cutoff.out.id. If present, the .king.bin file must be triangular (either precision is ok)." argument="--king-cutoff"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="king_cutoff_MOD_0_0" type="text" label=".king.bin + .king.id fileset prefix" value="" optional="False" argument=".king.bin + .king.id fileset prefix" help=""/> + <param name="king_cutoff_MOD_1_0" type="text" label="threshold" value="" optional="True" argument="threshold" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_write_covar"> + <param name="CONDITIONAL_SELECT_write_covar" type="select" label="Set Write covar" help="If covariates are defined, an updated version (with all filters applied) is automatically written to <output prefix>.cov whenever --make-pgen, --make-just-psam, --export, or a similar command is present. However, if you do not wish to simultaneously generate a new sample file, you can use --write-covar to just produce a pruned covariate file. Supported column sets are: maybefid: FID, if that column was in the input. fid: Force FID column to be written even when absent in the input. maybesid: SID, if that column was in the input. sid: Force SID column to be written even when absent in the input. maybeparents: Father/mother IIDs ('0' = missing), if columns in input. parents: Force PAT/MAT columns to be written even when absent in input. sex: '1' = male, '2' = female, 'NA' = missing. pheno1: First active phenotype. If none, all column entries are set to the --output-missing-phenotype string. phenos: All active phenotypes, if any. (Can be combined with pheno1 to force at least one phenotype column to be written.) (Covariates are always present, and positioned here.) The default is maybefid,maybesid." argument="--write-covar"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="write_covar_MOD_0_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <param name="write_samples" type="boolean" label="Write samples" truevalue="--write-samples" falsevalue="" optional="true" argument="--write-samples" help="Report IDs of all samples which pass your filters/inclusion thresholds." checked="False"/> + <conditional name="CONDITIONAL_write_snplist"> + <param name="CONDITIONAL_SELECT_write_snplist" type="select" label="Set Write snplist" help="List all variants which pass your filters/inclusion thresholds." argument="--write-snplist"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="write_snplist_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_glm"> + <param name="CONDITIONAL_SELECT_glm" type="select" label="Set Glm" help="[{genotypic | hethom | dominant | recessive}] ['interaction'] ['hide-covar'] ['intercept'] [{no-firth | firth-fallback | firth}] ['cols='<col set desc.>] ['local-covar='<file>] ['local-pvar='<file>] ['local-psam='<file>] ['local-omit-last' | 'local-cats='<category ct>] Basic association analysis on quantitative and/or case/control phenotypes. For each variant, a linear (for quantitative traits) or logistic (for case/control) regression is run with the phenotype as the dependent variable, and nonmajor allele dosage(s) and a constant-1 column as predictors. * There is usually an additive effect line for every nonmajor allele, and no such line for the major allele. To omit REF alleles instead of major alleles, add the 'omit-ref' modifier. (When performing interaction testing, this tends to cause the multicollinearity check to fail for low-ref-frequency variants.) * By default, sex (male = 1, female = 2; note that this is a change from PLINK 1.x) is automatically added as a predictor for X chromosome variants, and no others. The 'sex' modifier causes it to be added everywhere (except chrY), while 'no-x-sex' excludes it entirely. * The 'log10' modifier causes p-values to be reported in -log10(p) form. * 'pheno-ids' causes the samples used in each set of regressions to be written to an .id file. (When the samples differ on chrX or chrY, .x.id and/or .y.id files are also written.) * The 'genotypic' modifier adds an additive effect/dominance deviation 2df joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and 0..1..0 coding instead. * 'dominant' and 'recessive' specify a model assuming full dominance or recessiveness, respectively, for the ref allele. I.e. the genotype column is recoded as 0..1..1 or 0..0..1, respectively. * 'interaction' adds genotype x covariate interactions to the model. Note that this tends to produce 'NA' results (due to the multicollinearity check) when the reference allele is 'wrong'; --maj-ref can be used to enable analysis of those variants. * Additional predictors can be added with --covar. By default, association statistics are reported for all nonconstant predictors; 'hide-covar' suppresses covariate-only results, while 'intercept' causes intercepts to be reported. * For logistic regression, when the phenotype [quasi-]separates the genotype, an NA result is currently reported by default. To fall back on Firth logistic regression instead when the basic logistic regression fails to converge, add the 'firth-fallback' modifier (highly recommended, will become the default when beta testing begins). To eliminate the special case and use Firth logistic regression everywhere, add 'firth'. 'no-firth' can be used to prevent Firth regression from being attempted in a way that'll still work after alpha testing completes. * To add covariates which are not constant across all variants, add the 'local-covar=', 'local-pvar=', and 'local-psam=' modifiers, and use full filenames for each. Normally, the local-covar file should have c * n real-valued columns, where the first c columns correspond to the first sample in the local-psam file, columns (c+1) to 2c correspond to the second sample, etc.; and the mth line corresponds to the mth nonheader line of the local-pvar file. (Variants outside of the local-pvar file are excluded from the regression.) The local covariates are assigned the names LOCAL1, LOCAL2, etc.; to exclude the last local covariate from the regression (necessary if they are e.g. local ancestry coefficients which sum to 1), add 'local-omit-last'. Alternatively, with 'local-cats='<k>, the local-covar file is expected to have n columns with integer-valued entries in [1, k]. These category assignments are expanded into (k-1) local covariates in the usual manner. The main report supports the following column sets: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. (A1 is always present, and positioned here. For multiallelic variants, this column may contain multiple comma-separated alleles when the result doesn't depend on which allele is A1.) ax: Non-A1 alleles, comma-separated. a1count: A1 allele count (can be decimal with dosage data). totallele: Allele observation count (can be higher than --freq value, due to inclusion of het haploids and chrX model). a1countcc: A1 count in cases, then controls (case/control only). totallelecc: Case and control allele observation counts. gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases, then controls (case/control only). a1freq: A1 allele frequency. a1freqcc: A1 frequency in cases, then controls (case/control only). machr2: Unphased MaCH imputation quality (frequently labeled 'INFO'). firth: Reports whether Firth regression was used (firth-fallback only). test: Test identifier. (Required unless only one test is run.) nobs: Number of samples in the regression. beta: Regression coefficient (for A1 if additive test). orbeta: Odds ratio for case/control, beta for quantitative traits. (Ignored if 'beta' column set included.) se: Standard error of beta. ci: Bounds of symmetric approximate confidence interval (requires --ci). tz: T-statistic for linear regression, Wald Z-score for logistic/Firth. p: Asymptotic p-value (or -log10(p)) for T/Z-statistic. err: Error code for NA results. The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p." argument="--glm"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="glm_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="glm_MOD_1_0" type="text" label="'omit-ref'" value="" optional="False" argument="'omit-ref'" help=""/> + <conditional name="CONDITIONAL_glm_MOD_2"> + <param name="CONDITIONAL_SELECT_glm_MOD_2" type="select" label="How to set Glm"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="glm_MOD_2" type="select" label="Select value"> + <option value="{sex">{sex</option> +<option value="no-x-sex}">no-x-sex}</option> +</param> + </when> + </conditional> + <param name="glm_MOD_3_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/> + <param name="glm_MOD_4_0" type="text" label="'pheno-ids'" value="" optional="False" argument="'pheno-ids'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_score"> + <param name="CONDITIONAL_SELECT_score" type="select" label="Set Score" help="Apply linear scoring system(s) to each sample. The input file should have one line per scored variant. Variant IDs are read from column #i and allele codes are read from column #j, where i defaults to 1 and j defaults to i+1. For now, only one allele per multiallelic variant may be assigned an explicit score; contact us if you need this changed. * By default, a single column of input coefficients is read from column #k, where k defaults to j+1. (--score-col-nums can be used to specify multiple columns.) * 'header-read' causes the first line of the input file to be treated as a header line containing score names. Otherwise, score(s) are assigned the names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line to be entirely ignored. * By default, copies of unnamed alleles contribute zero to score, while missing genotypes contribute an amount proportional to the loaded (via --read-freq) or imputed allele frequency. To throw out missing observations instead (decreasing the denominator in the final average when this happens), use the 'no-mean-imputation' modifier. * You can use the 'center' modifier to shift all genotypes to mean zero, or 'variance-standardize' to linearly transform the genotypes to mean-0, variance-1. * The 'dominant' modifier causes dosages greater than 1 to be treated as 1, while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes. ('dominant', 'recessive', and 'variance-standardize' cannot be used with chrX.) * The 'se' modifier causes the input coefficients to be treated as independent standard errors; in this case, standard errors for the score average/sum are reported. (Note that this will systematically underestimate standard errors when scored variants are in LD.) * By default, --score errors out if a variant ID in the input file appears multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to skip them instead (a warning is still printed if such variants are present). * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to be written to <output prefix>.sscore.vars[.zst]. The main report supports the following column sets: maybefid: FID, if that column was in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was in the input. sid: Force SID column to be written even when absent in the input. pheno1: First active phenotype. phenos: All active phenotypes, if any. nmissallele: Number of nonmissing alleles. denom: Denominator of score average (equal to nmissallele value when 'no-mean-imputation' specified). dosagesum: Sum of named allele dosages. scoreavgs: Score averages. scoresums: Score sums. The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs. For more sophisticated polygenic risk scoring, we recommend the PRSice-2 software package (https://www.prsice.info/ )." argument="--score"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="score_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="score_MOD_1_0" type="text" label="i" value="" optional="False" argument="i" help=""/> + <param name="score_MOD_2_0" type="text" label="j" value="" optional="False" argument="j" help=""/> + <param name="score_MOD_3_0" type="text" label="k" value="" optional="False" argument="k" help=""/> + <conditional name="CONDITIONAL_score_MOD_4"> + <param name="CONDITIONAL_SELECT_score_MOD_4" type="select" label="How to set Score"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="score_MOD_4" type="select" label="Select value"> + <option value="{header">{header</option> +<option value="header-read}">header-read}</option> +</param> + </when> + </conditional> + <conditional name="CONDITIONAL_score_MOD_5"> + <param name="CONDITIONAL_SELECT_score_MOD_5" type="select" label="How to set Score"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="score_MOD_5" type="select" label="Select value"> + <option value="{center">{center</option> +<option value="variance-standardize">variance-standardize</option> +<option value="dominant">dominant</option> +<option value="recessive}">recessive}</option> +</param> + </when> + </conditional> + <param name="score_MOD_6_0" type="text" label="'no-mean-imputation'" value="" optional="False" argument="'no-mean-imputation'" help=""/> + <param name="score_MOD_7_0" type="text" label="'se'" value="" optional="False" argument="'se'" help=""/> + <param name="score_MOD_8_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="score_MOD_9_0" type="text" label="'ignore-dup-ids'" value="" optional="False" argument="'ignore-dup-ids'" help=""/> + <conditional name="CONDITIONAL_score_MOD_10"> + <param name="CONDITIONAL_SELECT_score_MOD_10" type="select" label="How to set Score"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="score_MOD_10" type="select" label="Select value"> + <option value="{list-variants">{list-variants</option> +<option value="list-variants-zs}">list-variants-zs}</option> +</param> + </when> + </conditional> + <param name="score_MOD_11_0" type="text" label="'cols='<col set descriptor>" value="" optional="False" argument="'cols='<col set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_variant_score"> + <param name="CONDITIONAL_SELECT_variant_score" type="select" label="Set Variant score" help="(alias: --vscore) Apply linear scoring system(s) to each variant. Each reported variant score is the dot product of a sample-weight vector with the total-ALT-dosage vector, with MAF-based mean imputation applied to missing dosages. Input file format: one line per sample, each starting with an ID and followed by scoring weight(s); it can also have a header line with the sample ID representation and the score name(s). The usual .vscore text report supports the following column sets: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. altfreq: ALT allele frequency used for mean-imputation. nmiss: Number of missing (and thus mean-imputed) dosages. nobs: Number of (nonmissing) sample observations. (Variant scores are always present, and positioned here.) Default is chrom,pos,ref,alt. If binary output is requested instead, the main .vscore.bin matrix contains double-precision floating-point values, column (score) ID(s) are saved to a <output prefix>.vscore.cols, and variant IDs are saved to <output prefix>.vscore.vars[.zst]." argument="--variant-score"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="variant_score_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="variant_score_MOD_1_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <conditional name="CONDITIONAL_variant_score_MOD_2"> + <param name="CONDITIONAL_SELECT_variant_score_MOD_2" type="select" label="How to set Variant score"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="variant_score_MOD_2" type="select" label="Select value"> + <option value="'bin'">'bin'</option> +<option value="'cols='<col set descriptor>">'cols='<col set descriptor></option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_file"> + <param name="CONDITIONAL_SELECT_adjust_file" type="select" label="Set Adjust file" help="Given a file with unfiltered association test results, report some basic multiple-testing corrections, sorted in increasing-p-value order. * 'gc' causes genomic-controlled p-values to be used in the formulas. (This tends to be overly conservative. We note that LD Score regression usually does a better job of calibrating lambda; see Lee JJ, McGue M, Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an estimator of confounding and genetic correlations in genome-wide association studies.) * 'log10' causes negative base 10 logs of p-values to be reported, instead of raw p-values. 'input-log10' specifies that the input file contains -log10(p) values. * If the input file contains multiple tests per variant which are distinguished by a 'TEST' column (true for --linear/--logistic/--glm), you must use 'test=' to select the test to process. The following column sets are supported: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. a1: Tested allele. (Omitted if missing from input file.) unadj: Unadjusted p-value. gc: Devlin & Roeder (1999) genomic control corrected p-value (additive models only). qq: P-value quantile. bonf: Bonferroni correction. holm: Holm-Bonferroni (1979) adjusted p-value. sidakss: Sidak single-step adjusted p-value. sidaksd: Sidak step-down adjusted p-value. fdrbh: Benjamini & Hochberg (1995) step-up false discovery control. fdrby: Benjamini & Yekutieli (2001) step-up false discovery control. Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby." argument="--adjust-file"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_file_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="adjust_file_MOD_1_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="adjust_file_MOD_2_0" type="text" label="'gc'" value="" optional="False" argument="'gc'" help=""/> + <param name="adjust_file_MOD_3_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + <param name="adjust_file_MOD_4_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/> + <param name="adjust_file_MOD_5_0" type="text" label="'input-log10'" value="" optional="False" argument="'input-log10'" help=""/> + <param name="adjust_file_MOD_6_0" type="text" label="'test='<test name, case-sensitive>" value="" optional="False" argument="'test='<test name, case-sensitive>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_genotyping_rate"> + <param name="CONDITIONAL_SELECT_genotyping_rate" type="select" label="Set Genotyping rate" help="Report genotyping rate in log (this was automatic in PLINK 1.x)." argument="--genotyping-rate"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="genotyping_rate_MOD_0_0" type="text" label="'dosage'" value="" optional="False" argument="'dosage'" help=""/> + </when> + </conditional> + <param name="pgen_info" type="boolean" label="Pgen info" truevalue="--pgen-info" falsevalue="" optional="true" argument="--pgen-info" help="Reports basic information about a .pgen file." checked="False"/> + <param name="validate" type="boolean" label="Validate" truevalue="--validate" falsevalue="" optional="true" argument="--validate" help="Validates all variant records in a .pgen file." checked="False"/> + <conditional name="CONDITIONAL_zst_decompress"> + <param name="CONDITIONAL_SELECT_zst_decompress" type="select" label="Set Zst decompress" help="(alias: --zd) Decompress a Zstd-compressed file. If no output filename is specified, the file is decompressed to standard output. This cannot be used with any other flags, and does not cause a log file to be generated." argument="--zst-decompress"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="zst_decompress_MOD_0_0" type="text" label=".zst file" value="" optional="True" argument=".zst file" help=""/> + <param name="zst_decompress_MOD_1_0" type="text" label="output filename" value="" optional="False" argument="output filename" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_silent"> + <param name="CONDITIONAL_SELECT_silent" type="select" label="Set Silent" help="Suppress regular output to console. (Error-output is not suppressed.) " argument="--silent"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_double_id"> + <param name="CONDITIONAL_SELECT_double_id" type="select" label="Set Double id" help="Set both FIDs and IIDs to the VCF/.bgen sample ID. " argument="--double-id"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_const_fid"> + <param name="CONDITIONAL_SELECT_const_fid" type="select" label="Set Const fid" help="Set all FIDs to the given constant. If '0' (the default), no FID column is created. " argument="--const-fid"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="const_fid_MOD_0_0" type="text" label="ID" value="" optional="False" argument="ID" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_id_delim"> + <param name="CONDITIONAL_SELECT_id_delim" type="select" label="Set Id delim" help="Normally parses single-delimiter sample IDs as <FID><d><IID>, and double-delimiter IDs as <FID><d><IID><d><SID>; default delimiter is '_'. --id-delim can no longer be used with --double-id/--const-fid; it will error out if any ID lacks the delimiter. " argument="--id-delim"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="id_delim_MOD_0_0" type="text" label="d" value="" optional="False" argument="d" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_idspace_to"> + <param name="CONDITIONAL_SELECT_idspace_to" type="select" label="Set Idspace to" help="Convert spaces in VCF/.bgen sample IDs to the given character. " argument="--idspace-to"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="idspace_to_MOD_0_0" type="text" label="c" value="" optional="True" argument="c" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_iid_sid"> + <param name="CONDITIONAL_SELECT_iid_sid" type="select" label="Set Iid sid" help="Make --id-delim and --sample-diff interpret two-token sample IDs as IID-SID instead of FID-IID. " argument="--iid-sid"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_vcf_require_gt"> + <param name="CONDITIONAL_SELECT_vcf_require_gt" type="select" label="Set Vcf require gt" help="Skip variants with no GT field. " argument="--vcf-require-gt"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_vcf_min_gq"> + <param name="CONDITIONAL_SELECT_vcf_min_gq" type="select" label="Set Vcf min gq" help="No-call genotypes when GQ is present and below the threshold. " argument="--vcf-min-gq"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vcf_min_gq_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_vcf_max_dp"> + <param name="CONDITIONAL_SELECT_vcf_max_dp" type="select" label="Set Vcf max dp" help="No-call genotypes when DP is present and above/below " argument="--vcf-max-dp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vcf_max_dp_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_vcf_min_dp"> + <param name="CONDITIONAL_SELECT_vcf_min_dp" type="select" label="Set Vcf min dp" help="" argument="--vcf-min-dp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vcf_min_dp_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_vcf_half_call"> + <param name="CONDITIONAL_SELECT_vcf_half_call" type="select" label="Set Vcf half call" help="Specify how '0/.' and similar VCF GT values should be handled. The following four modes are supported: * 'error'/'e' (default) errors out and reports line #. * 'haploid'/'h' treats them as haploid calls. * 'missing'/'m' treats them as missing. * 'reference'/'r' treats the missing value as 0. " argument="--vcf-half-call"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vcf_half_call_MOD_0_0" type="text" label="m" value="" optional="True" argument="m" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_oxford_single_chr"> + <param name="CONDITIONAL_SELECT_oxford_single_chr" type="select" label="Set Oxford single chr" help="Specify single-chromosome .gen/.bgen file with no useful chromosome info inside. " argument="--oxford-single-chr"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="oxford_single_chr_MOD_0_0" type="text" label="chr name" value="" optional="True" argument="chr name" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_missing_code"> + <param name="CONDITIONAL_SELECT_missing_code" type="select" label="Set Missing code" help="Comma-delimited list of missing phenotype (alias: --missing_code) values for Oxford-format import (default 'NA')." argument="--missing-code"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="missing_code_MOD_0_0" type="text" label="string list" value="" optional="False" argument="string list" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_hard_call_threshold"> + <param name="CONDITIONAL_SELECT_hard_call_threshold" type="select" label="Set Hard call threshold" help="When importing dosage data, a hardcall is normally saved when the distance from the nearest hardcall, defined as 0.5 * sum_i |x_i - round(x_i)| (where the x_i's are 0..2 allele dosages), is not greater than 0.1. You can adjust this threshold by providing a numeric parameter to --hard-call-threshold. You can also use this with --make-[b]pgen to alter the saved hardcalls while leaving the dosages untouched, or --make-bed to tweak hardcall export. " argument="--hard-call-threshold"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="hard_call_threshold_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_dosage_erase_threshold"> + <param name="CONDITIONAL_SELECT_dosage_erase_threshold" type="select" label="Set Dosage erase threshold" help="--hard-call-threshold normally preserves the original dosages, and several PLINK 2 commands use them when they're available. Use --dosage-erase-threshold to make PLINK 2 erase dosages and keep only hardcalls when distance-from-hardcall <= the given level. " argument="--dosage-erase-threshold"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="dosage_erase_threshold_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_import_dosage_certainty"> + <param name="CONDITIONAL_SELECT_import_dosage_certainty" type="select" label="Set Import dosage certainty" help="The PLINK 2 file format currently supports a single dosage for each allele. Some other dosage file formats include a separate probability for every possible genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52, P(1/1)=0.28}, a highly uncertain call that is nevertheless treated as a hardcall under '--hard-call-threshold 0.1'. To make PLINK 2 treat a dosage as missing whenever the largest probability is less than a threshold, use --import-dosage-certainty. " argument="--import-dosage-certainty"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="import_dosage_certainty_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_input_missing_genotype"> + <param name="CONDITIONAL_SELECT_input_missing_genotype" type="select" label="Set Input missing genotype" help="'.' is always interpreted as a missing genotype code in input files. By default, '0' also is; you can change this second missing code with --input-missing-genotype. " argument="--input-missing-genotype"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="input_missing_genotype_MOD_0_0" type="text" label="c" value="" optional="True" argument="c" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_allow_extra_chr"> + <param name="CONDITIONAL_SELECT_allow_extra_chr" type="select" label="Set Allow extra chr" help="Permit unrecognized chromosome codes (alias --aec). " argument="--allow-extra-chr"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_chr_set"> + <param name="CONDITIONAL_SELECT_chr_set" type="select" label="Set Chr set" help="Specify a nonhuman chromosome set. The first parameter sets the number of diploid autosome pairs if positive, or haploid chromosomes if negative. Given diploid autosomes, the remaining modifiers indicate the absence of the named non-autosomal chromosomes." argument="--chr-set"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="chr_set_MOD_0_0" type="text" label="autosome ct" value="" optional="True" argument="autosome ct" help=""/> + <param name="chr_set_MOD_1_0" type="text" label="'no-x'" value="" optional="False" argument="'no-x'" help=""/> + <param name="chr_set_MOD_2_0" type="text" label="'no-y'" value="" optional="False" argument="'no-y'" help=""/> + <param name="chr_set_MOD_3_0" type="text" label="'no-xy'" value="" optional="False" argument="'no-xy'" help=""/> + <param name="chr_set_MOD_4_0" type="text" label="'no-mt'" value="" optional="False" argument="'no-mt'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_cow"> + <param name="CONDITIONAL_SELECT_cow" type="select" label="Set Cow" help="Shortcuts for those species. " argument="--cow"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_dog"> + <param name="CONDITIONAL_SELECT_dog" type="select" label="Set Dog" help="Shortcuts for those species. " argument="--dog"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_horse"> + <param name="CONDITIONAL_SELECT_horse" type="select" label="Set Horse" help="Shortcuts for those species. " argument="--horse"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_mouse"> + <param name="CONDITIONAL_SELECT_mouse" type="select" label="Set Mouse" help="Shortcuts for those species. " argument="--mouse"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_rice"> + <param name="CONDITIONAL_SELECT_rice" type="select" label="Set Rice" help="Shortcuts for those species. " argument="--rice"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_sheep"> + <param name="CONDITIONAL_SELECT_sheep" type="select" label="Set Sheep" help="Shortcuts for those species. " argument="--sheep"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_autosome_num"> + <param name="CONDITIONAL_SELECT_autosome_num" type="select" label="Set Autosome num" help="Alias for '--chr-set <value> no-y no-xy no-mt'. " argument="--autosome-num"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="autosome_num_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_human"> + <param name="CONDITIONAL_SELECT_human" type="select" label="Set Human" help="Explicitly specify human chromosome set, and make output .pvar/VCF files include a ##chrSet header line. (.pvar/VCF output files automatically include ##chrSet when a nonhuman set is specified.) " argument="--human"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_chr_override"> + <param name="CONDITIONAL_SELECT_chr_override" type="select" label="Set Chr override" help="By default, if --chr-set/--autosome-num/--cow/etc. conflicts with an input file ##chrSet header line, PLINK 2 will error out. --chr-override with no parameter causes the command line to take precedence; '--chr-override file' defers to the file. " argument="--chr-override"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="chr_override_MOD_0_0" type="text" label="'file'" value="" optional="False" argument="'file'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_var_min_qual"> + <param name="CONDITIONAL_SELECT_var_min_qual" type="select" label="Set Var min qual" help="Skip variants with low/missing QUAL. " argument="--var-min-qual"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="var_min_qual_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_var_filter"> + <param name="CONDITIONAL_SELECT_var_filter" type="select" label="Set Var filter" help="Skip variants which have FILTER failures. " argument="--var-filter"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="var_filter_MOD_0_0" type="text" label="exception(s)..." value="" optional="False" argument="exception(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract_if_info"> + <param name="CONDITIONAL_SELECT_extract_if_info" type="select" label="Set Extract if info" help="Exclude variants which don't/do satisfy " argument="--extract-if-info"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="extract_if_info_MOD_0_0" type="text" label="key" value="" optional="True" argument="key" help=""/> + <param name="extract_if_info_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/> + <param name="extract_if_info_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_exclude_if_info"> + <param name="CONDITIONAL_SELECT_exclude_if_info" type="select" label="Set Exclude if info" help='(aliases: --extract-if, e.g. --exclude-if) --extract-if-info "VT == SNP" Unless the operator is !=, the predicate always evaluates to false when the key is missing.' argument="--exclude-if-info"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="exclude_if_info_MOD_0_0" type="text" label="key" value="" optional="True" argument="key" help=""/> + <param name="exclude_if_info_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/> + <param name="exclude_if_info_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_require_info"> + <param name="CONDITIONAL_SELECT_require_info" type="select" label="Set Require info" help="Exclude variants based on nonexistence " argument="--require-info"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="require_info_MOD_0_0" type="text" label="key(s)..." value="" optional="True" argument="key(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_require_no_info"> + <param name="CONDITIONAL_SELECT_require_no_info" type="select" label="Set Require no info" help="" argument="--require-no-info"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="require_no_info_MOD_0_0" type="text" label="key(s)..." value="" optional="True" argument="key(s)..." help="Multiple values are allowed"/> + <param name="require_no_info_MOD_1_0" type="text" label="key" value="" optional="True" argument="key" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract_col_cond"> + <param name="CONDITIONAL_SELECT_extract_col_cond" type="select" label="Set Extract col cond" help="" argument="--extract-col-cond"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="extract_col_cond_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/> + <param name="extract_col_cond_MOD_1_0" type="text" label="valcol" value="" optional="False" argument="valcol" help=""/> + <param name="extract_col_cond_MOD_2_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/> + <param name="extract_col_cond_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract_col_cond_match"> + <param name="CONDITIONAL_SELECT_extract_col_cond_match" type="select" label="Set Extract col cond match" help="" argument="--extract-col-cond-match"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="extract_col_cond_match_MOD_0_0" type="text" label="(sub)string(s)..." value="" optional="True" argument="(sub)string(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract_col_cond_mismatch"> + <param name="CONDITIONAL_SELECT_extract_col_cond_mismatch" type="select" label="Set Extract col cond mismatch" help="" argument="--extract-col-cond-mismatch"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="extract_col_cond_mismatch_MOD_0_0" type="text" label="(sub)string(s)..." value="" optional="True" argument="(sub)string(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <param name="extract_col_cond_substr" type="boolean" label="Extract col cond substr" truevalue="--extract-col-cond-substr" falsevalue="" optional="true" argument="--extract-col-cond-substr" help="" checked="False"/> + <conditional name="CONDITIONAL_extract_col_cond_min"> + <param name="CONDITIONAL_SELECT_extract_col_cond_min" type="select" label="Set Extract col cond min" help="" argument="--extract-col-cond-min"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="extract_col_cond_min_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract_col_cond_max"> + <param name="CONDITIONAL_SELECT_extract_col_cond_max" type="select" label="Set Extract col cond max" help="Exclude all variants without a value-column entry satisfying a condition. * By default, values are read from column 2 of the file, and variant IDs are read from column 1. * Three types of conditions are supported: * When --extract-col-cond-match is specified without --extract-col-cond-substr, the value is checked for equality with the given strings, and kept iff one of them matches. Similarly, --extract-col-cond-mismatch without --extract-col-cond-substr causes the variant to be kept iff the value matches none of the given strings. * When --extract-col-cond-match and/or -mismatch are specified with --extract-col-cond-substr, the variant is kept iff none of the --extract-col-cond-mismatch substrings are contained in the value, and either --extract-col-cond-match was unspecified or at least one of its substrings is contained. * Otherwise, the value is interpreted as a number, and the variant is kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX)." argument="--extract-col-cond-max"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="extract_col_cond_max_MOD_0_0" type="text" label="max" value="" optional="True" argument="max" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_pheno"> + <param name="CONDITIONAL_SELECT_pheno" type="select" label="Set Pheno" help="Specify additional phenotype/covariate file. Comma-delimited files with a header line are now permitted. " argument="--pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pheno_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/> + <param name="pheno_MOD_1_0" type="data" format="plink.pheno" label="f" multiple="False" optional="True" argument="f"/> + </when> + </conditional> + <conditional name="CONDITIONAL_pheno_name"> + <param name="CONDITIONAL_SELECT_pheno_name" type="select" label="Set Pheno name" help="Only load the designated phenotype(s) from the --pheno (if one was specified) or .psam (if no --pheno) file. Separate multiple names with spaces or commas, and use dashes to designate ranges. " argument="--pheno-name"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pheno_name_MOD_0_0" type="text" label="name..." value="" optional="True" argument="name..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_pheno_col_nums"> + <param name="CONDITIONAL_SELECT_pheno_col_nums" type="select" label="Set Pheno col nums" help="Only load the phenotype(s) in the designated column number(s) from the --pheno file. " argument="--pheno-col-nums"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pheno_col_nums_MOD_0_0" type="text" label="#..." value="" optional="True" argument="#..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_no_psam_pheno"> + <param name="CONDITIONAL_SELECT_no_psam_pheno" type="select" label="Set No psam pheno" help="Ignore phenotype(s) in .psam/.fam file. " argument="--no-psam-pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_strict_sid0"> + <param name="CONDITIONAL_SELECT_strict_sid0" type="select" label="Set Strict sid0" help="By default, if there is no SID column in the .psam/.fam (or --update-ids) file, but there is one in another input file (for e.g. --keep/--remove), the latter SID column is ignored; sample IDs are considered matching as long as FID and IID are equal (with missing FID treated as '0'). If you also want to require SID = '0' for a sample ID match in this situation, add --strict-sid0. " argument="--strict-sid0"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_input_missing_phenotype"> + <param name="CONDITIONAL_SELECT_input_missing_phenotype" type="select" label="Set Input missing phenotype" help="Set nonzero number to treat as a missing pheno/covar in input files (default -9). " argument="--input-missing-phenotype"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="input_missing_phenotype_MOD_0_0" type="text" label="v" value="" optional="True" argument="v" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_no_input_missing_phenotype"> + <param name="CONDITIONAL_SELECT_no_input_missing_phenotype" type="select" label="Set No input missing phenotype" help="Don't treat any nonzero number as a missing pheno/covar. ('NA'/'nan' are still treated as missing.) " argument="--no-input-missing-phenotype"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_GALAXY_1"> + <param name="CONDITIONAL_SELECT_GALAXY_1" type="select" label="Set 1" help="Expect case/control phenotypes in input files to be coded as 0 = control, 1 = case, instead of the usual 0 = missing, 1 = ctrl, 2 = case. (Unlike PLINK 1.x, this does not force all phenotypes to be interpreted as case/ctrl.) " argument="--1"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_missing_catname"> + <param name="CONDITIONAL_SELECT_missing_catname" type="select" label="Set Missing catname" help="Set missing-categorical-phenotype string (case-sensitive, default 'NONE'). " argument="--missing-catname"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="missing_catname_MOD_0_0" type="text" label="str" value="" optional="True" argument="str" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_covar"> + <param name="CONDITIONAL_SELECT_covar" type="select" label="Set Covar" help="Specify additional covariate file. Comma-delimited files with a header line are now permitted. " argument="--covar"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="covar_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/> + <param name="covar_MOD_1_0" type="data" format="plink.covar" label="f" multiple="False" optional="True" argument="f"/> + </when> + </conditional> + <conditional name="CONDITIONAL_covar_name"> + <param name="CONDITIONAL_SELECT_covar_name" type="select" label="Set Covar name" help="Only load the designated covariate(s) from the --covar (if one was specified), --pheno (if no --covar), or .psam (if no --covar or --pheno) file. " argument="--covar-name"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="covar_name_MOD_0_0" type="text" label="name..." value="" optional="True" argument="name..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_covar_col_nums"> + <param name="CONDITIONAL_SELECT_covar_col_nums" type="select" label="Set Covar col nums" help="Only load the covariate(s) in the designated column number(s) from the --covar (if one was specified) or --pheno (if no --covar) file. " argument="--covar-col-nums"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="covar_col_nums_MOD_0_0" type="text" label="#..." value="" optional="True" argument="#..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_within"> + <param name="CONDITIONAL_SELECT_within" type="select" label="Set Within" help="Import a PLINK 1.x categorical phenotype. (Phenotype name defaults to 'CATPHENO'.) * If any numeric values are present, ALL values must be numeric. In that case, 'C' is added in front of all category names. * 'NA' is treated as a missing value. " argument="--within"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="within_MOD_0_0" type="data" format="tabular" label="f" multiple="False" optional="True" argument="f"/> + <param name="within_MOD_1_0" type="text" label="new pheno name" value="" optional="False" argument="new pheno name" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_mwithin"> + <param name="CONDITIONAL_SELECT_mwithin" type="select" label="Set Mwithin" help="Load --within categories from column n+2. " argument="--mwithin"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="mwithin_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_family"> + <param name="CONDITIONAL_SELECT_family" type="select" label="Set Family" help="Create a categorical phenotype from FID. Restrictions on and handling of numeric values are the same as for --within. " argument="--family"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="family_MOD_0_0" type="text" label="new pheno name" value="" optional="False" argument="new pheno name" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_family_missing_catname"> + <param name="CONDITIONAL_SELECT_family_missing_catname" type="select" label="Set Family missing catname" help="Make --family treat the specified FID as missing. " argument="--family-missing-catname"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="family_missing_catname_MOD_0_0" type="text" label="nm" value="" optional="True" argument="nm" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep"> + <param name="CONDITIONAL_SELECT_keep" type="select" label="Set Keep" help="Exclude all samples not named in a file. " argument="--keep"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_MOD_0_0" type="text" label="fname..." value="" optional="True" argument="fname..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_remove"> + <param name="CONDITIONAL_SELECT_remove" type="select" label="Set Remove" help="Exclude all samples named in a file. " argument="--remove"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="remove_MOD_0_0" type="text" label="fname..." value="" optional="True" argument="fname..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_fam"> + <param name="CONDITIONAL_SELECT_keep_fam" type="select" label="Set Keep fam" help="Exclude all families not named in a file. " argument="--keep-fam"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_fam_MOD_0_0" type="text" label="fn..." value="" optional="True" argument="fn..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_remove_fam"> + <param name="CONDITIONAL_SELECT_remove_fam" type="select" label="Set Remove fam" help="Exclude all families named in a file. " argument="--remove-fam"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="remove_fam_MOD_0_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract"> + <param name="CONDITIONAL_SELECT_extract" type="select" label="Set Extract" help="Usually excludes all variants (not) named " argument="--extract"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <conditional name="CONDITIONAL_extract_MOD_0"> + <param name="CONDITIONAL_SELECT_extract_MOD_0" type="select" label="How to set Extract"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="extract_MOD_0" type="select" label="Select value"> + <option value="{bed0">{bed0</option> +<option value="bed1}">bed1}</option> +</param> + </when> + </conditional> + <param name="extract_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_exclude"> + <param name="CONDITIONAL_SELECT_exclude" type="select" label="Set Exclude" help="" argument="--exclude"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <conditional name="CONDITIONAL_exclude_MOD_0"> + <param name="CONDITIONAL_SELECT_exclude_MOD_0" type="select" label="How to set Exclude"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="exclude_MOD_0" type="select" label="Select value"> + <option value="{bed0">{bed0</option> +<option value="bed1}">bed1}</option> +</param> + </when> + </conditional> + <param name="exclude_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_extract_intersect"> + <param name="CONDITIONAL_SELECT_extract_intersect" type="select" label="Set Extract intersect" help="Just like --extract, except that a variant must be in the intersection, rather than just the union, of the files to remain. " argument="--extract-intersect"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <conditional name="CONDITIONAL_extract_intersect_MOD_0"> + <param name="CONDITIONAL_SELECT_extract_intersect_MOD_0" type="select" label="How to set Extract intersect"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="extract_intersect_MOD_0" type="select" label="Select value"> + <option value="{bed0">{bed0</option> +<option value="bed1}">bed1}</option> +</param> + </when> + </conditional> + <param name="extract_intersect_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_cats"> + <param name="CONDITIONAL_SELECT_keep_cats" type="select" label="Set Keep cats" help="These can be used individually or in combination " argument="--keep-cats"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_cats_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_cat_names"> + <param name="CONDITIONAL_SELECT_keep_cat_names" type="select" label="Set Keep cat names" help="" argument="--keep-cat-names"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_cat_names_MOD_0_0" type="text" label="nm..." value="" optional="True" argument="nm..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_cat_pheno"> + <param name="CONDITIONAL_SELECT_keep_cat_pheno" type="select" label="Set Keep cat pheno" help="If more than one categorical phenotype is loaded, or you wish to filter on a categorical covariate, --keep-cat-pheno must be used to specify which phenotype/covariate --keep-cats and --keep-cat-names apply to. " argument="--keep-cat-pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_cat_pheno_MOD_0_0" type="text" label="pheno" value="" optional="True" argument="pheno" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_remove_cats"> + <param name="CONDITIONAL_SELECT_remove_cats" type="select" label="Set Remove cats" help="Exclude all categories named in the file. " argument="--remove-cats"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="remove_cats_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + </when> + </conditional> + <conditional name="CONDITIONAL_remove_cat_names"> + <param name="CONDITIONAL_SELECT_remove_cat_names" type="select" label="Set Remove cat names" help="Exclude named categories. " argument="--remove-cat-names"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="remove_cat_names_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_remove_cat_pheno"> + <param name="CONDITIONAL_SELECT_remove_cat_pheno" type="select" label="Set Remove cat pheno" help="Specify pheno for --remove-cats/remove-cat-names. " argument="--remove-cat-pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="remove_cat_pheno_MOD_0_0" type="text" label="phe" value="" optional="True" argument="phe" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_split_cat_pheno"> + <param name="CONDITIONAL_SELECT_split_cat_pheno" type="select" label="Set Split cat pheno" help="Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last') binary phenotypes, with names of the form <orig. pheno name>=<cat. name>. (As a consequence, affected phenotypes and categories are not permitted to contain the '=' character.) * This happens after all sample filters. * If no phenotype or covariate names are provided, all categorical phenotypes (but not covariates) are processed. * By default, generated covariates are coded as 1=false, 2=true. To code them as 0=false, 1=true instead, add the 'covar-01' modifier." argument="--split-cat-pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <conditional name="CONDITIONAL_split_cat_pheno_MOD_0"> + <param name="CONDITIONAL_SELECT_split_cat_pheno_MOD_0" type="select" label="How to set Split cat pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="split_cat_pheno_MOD_0" type="select" label="Select value"> + <option value="{omit-most">{omit-most</option> +<option value="omit-last}">omit-last}</option> +</param> + </when> + </conditional> + <param name="split_cat_pheno_MOD_1_0" type="text" label="'covar-01'" value="" optional="False" argument="'covar-01'" help=""/> + <param name="split_cat_pheno_MOD_2_0" type="text" label="cat. pheno/covar name(s)..." value="" optional="False" argument="cat. pheno/covar name(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_loop_cats"> + <param name="CONDITIONAL_SELECT_loop_cats" type="select" label="Set Loop cats" help="Run variant filters and subsequent operations on just the samples in the first category; then just the samples in the second category; and so on, for all categories in the named categorical phenotype. " argument="--loop-cats"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="loop_cats_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_no_id_header"> + <param name="CONDITIONAL_SELECT_no_id_header" type="select" label="Set No id header" help="Don't include a header line in .id output files. This normally forces two-column FID/IID output; add 'iid-only' to force just single-column IID. " argument="--no-id-header"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="no_id_header_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_variance_standardize"> + <param name="CONDITIONAL_SELECT_variance_standardize" type="select" label="Set Variance standardize" help="" argument="--variance-standardize"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="variance_standardize_MOD_0_0" type="text" label="pheno/covar name(s)..." value="" optional="False" argument="pheno/covar name(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_covar_variance_standardize"> + <param name="CONDITIONAL_SELECT_covar_variance_standardize" type="select" label="Set Covar variance standardize" help="Linearly transform named covariates (and quantitative phenotypes, if --variance-standardize) to mean-zero, variance 1. If no parameters are provided, all possible phenotypes/covariates are affected. This is frequently necessary to prevent multicollinearity when dealing with covariates where abs(mean) is much larger than abs(standard deviation), such as year of birth." argument="--covar-variance-standardize"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="covar_variance_standardize_MOD_0_0" type="text" label="covar name(s)..." value="" optional="False" argument="covar name(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_quantile_normalize"> + <param name="CONDITIONAL_SELECT_quantile_normalize" type="select" label="Set Quantile normalize" help="Force named covariates and quantitative " argument="--quantile-normalize"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_pheno_quantile_normalize"> + <param name="CONDITIONAL_SELECT_pheno_quantile_normalize" type="select" label="Set Pheno quantile normalize" help="" argument="--pheno-quantile-normalize"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pheno_quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_covar_quantile_normalize"> + <param name="CONDITIONAL_SELECT_covar_quantile_normalize" type="select" label="Set Covar quantile normalize" help="" argument="--covar-quantile-normalize"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="covar_quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_chr"> + <param name="CONDITIONAL_SELECT_chr" type="select" label="Set Chr" help="Exclude all variants not on the given chromosome(s). Valid choices for humans are 0 (unplaced), 1-22, X, Y, XY, MT, PAR1, and PAR2. Separate multiple chromosomes with spaces and/or commas, and use a dash (no adjacent spaces permitted) to denote a range, e.g. '--chr 1-4, 22, par1, x, par2'. " argument="--chr"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="chr_MOD_0_0" type="text" label="chr(s)..." value="" optional="True" argument="chr(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_not_chr"> + <param name="CONDITIONAL_SELECT_not_chr" type="select" label="Set Not chr" help="Reverse of --chr (exclude variants on listed chromosomes). " argument="--not-chr"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="not_chr_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_autosome"> + <param name="CONDITIONAL_SELECT_autosome" type="select" label="Set Autosome" help="Exclude all non-autosomal variants. " argument="--autosome"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_autosome_par"> + <param name="CONDITIONAL_SELECT_autosome_par" type="select" label="Set Autosome par" help="Exclude all non-autosomal variants, except those in a pseudo-autosomal region. " argument="--autosome-par"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_snps_only"> + <param name="CONDITIONAL_SELECT_snps_only" type="select" label="Set Snps only" help="Exclude non-SNP variants. By default, SNP = all allele codes are single-character (so multiallelic variants with a mix of SNPs and non-SNPs are excluded; split your variants first if that's a problem). The 'just-acgt' modifier restricts SNP codes to {A,C,G,T,a,c,g,t,<missing>}. " argument="--snps-only"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="snps_only_MOD_0_0" type="text" label="'just-acgt'" value="" optional="False" argument="'just-acgt'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_from"> + <param name="CONDITIONAL_SELECT_from" type="select" label="Set From" help="Use ID(s) to specify a variant range to load. When used " argument="--from"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="from_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_to"> + <param name="CONDITIONAL_SELECT_to" type="select" label="Set To" help="" argument="--to"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="to_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_snp"> + <param name="CONDITIONAL_SELECT_snp" type="select" label="Set Snp" help="Specify a single variant to load. " argument="--snp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="snp_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_exclude_snp"> + <param name="CONDITIONAL_SELECT_exclude_snp" type="select" label="Set Exclude snp" help="Specify a single variant to exclude. " argument="--exclude-snp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="exclude_snp_MOD_0_0" type="text" label="ID" value="" optional="True" argument="ID" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_window"> + <param name="CONDITIONAL_SELECT_window" type="select" label="Set Window" help="With --snp/--exclude-snp, loads/excludes all variants within half the specified kb distance of the named one. " argument="--window"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="window_MOD_0_0" type="text" label="kbs" value="" optional="True" argument="kbs" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_from_bp"> + <param name="CONDITIONAL_SELECT_from_bp" type="select" label="Set From bp" help="Use base-pair coordinates to define a variant range to " argument="--from-bp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="from_bp_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_to_bp"> + <param name="CONDITIONAL_SELECT_to_bp" type="select" label="Set To bp" help="" argument="--to-bp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="to_bp_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_from_kb"> + <param name="CONDITIONAL_SELECT_from_kb" type="select" label="Set From kb" help="" argument="--from-kb"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="from_kb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_to_kb"> + <param name="CONDITIONAL_SELECT_to_kb" type="select" label="Set To kb" help="" argument="--to-kb"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="to_kb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_from_mb"> + <param name="CONDITIONAL_SELECT_from_mb" type="select" label="Set From mb" help="" argument="--from-mb"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="from_mb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_to_mb"> + <param name="CONDITIONAL_SELECT_to_mb" type="select" label="Set To mb" help="" argument="--to-mb"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="to_mb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_snps"> + <param name="CONDITIONAL_SELECT_snps" type="select" label="Set Snps" help="Use IDs to specify variant range(s) to load or " argument="--snps"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="snps_MOD_0_0" type="text" label="var IDs..." value="" optional="True" argument="var IDs..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_exclude_snps"> + <param name="CONDITIONAL_SELECT_exclude_snps" type="select" label="Set Exclude snps" help="" argument="--exclude-snps"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="exclude_snps_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_force_intersect"> + <param name="CONDITIONAL_SELECT_force_intersect" type="select" label="Set Force intersect" help="PLINK 2 normally errors out when multiple variant inclusion filters (--extract, --extract-col-cond, --extract-intersect, --from/--to, --from-bp/--to-bp, --snp, --snps) are specified. --force-intersect allows the run to proceed; the set intersection will be taken. " argument="--force-intersect"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_thin"> + <param name="CONDITIONAL_SELECT_thin" type="select" label="Set Thin" help="Randomly remove variants, retaining each with prob. p. " argument="--thin"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="thin_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_thin_count"> + <param name="CONDITIONAL_SELECT_thin_count" type="select" label="Set Thin count" help="Randomly remove variants until n of them remain. " argument="--thin-count"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="thin_count_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_bp_space"> + <param name="CONDITIONAL_SELECT_bp_space" type="select" label="Set Bp space" help="Remove variants so that each pair is no closer than the given bp distance. " argument="--bp-space"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="bp_space_MOD_0_0" type="text" label="bps" value="" optional="True" argument="bps" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_thin_indiv"> + <param name="CONDITIONAL_SELECT_thin_indiv" type="select" label="Set Thin indiv" help="Randomly remove samples, retaining with prob. p. " argument="--thin-indiv"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="thin_indiv_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_thin_indiv_count"> + <param name="CONDITIONAL_SELECT_thin_indiv_count" type="select" label="Set Thin indiv count" help="Randomly remove samples until n of them remain. " argument="--thin-indiv-count"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="thin_indiv_count_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_col_match"> + <param name="CONDITIONAL_SELECT_keep_col_match" type="select" label="Set Keep col match" help="Exclude all samples without a 3rd column entry in the given file exactly matching one of the given strings. (Separate multiple strings with spaces.) " argument="--keep-col-match"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_col_match_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/> + <param name="keep_col_match_MOD_1_0" type="text" label="val(s)..." value="" optional="True" argument="val(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_col_match_name"> + <param name="CONDITIONAL_SELECT_keep_col_match_name" type="select" label="Set Keep col match name" help="Check column with given name instead. " argument="--keep-col-match-name"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_col_match_name_MOD_0_0" type="text" label="col name" value="" optional="True" argument="col name" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_col_match_num"> + <param name="CONDITIONAL_SELECT_keep_col_match_num" type="select" label="Set Keep col match num" help="Check nth column instead. " argument="--keep-col-match-num"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_col_match_num_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_geno"> + <param name="CONDITIONAL_SELECT_geno" type="select" label="Set Geno" help="" argument="--geno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="geno_MOD_0_0" type="text" label="val" value="" optional="False" argument="val" help=""/> + <conditional name="CONDITIONAL_geno_MOD_1"> + <param name="CONDITIONAL_SELECT_geno_MOD_1" type="select" label="How to set Geno"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="geno_MOD_1" type="select" label="Select value"> + <option value="{dosage">{dosage</option> +<option value="hh-missing}">hh-missing}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_mind"> + <param name="CONDITIONAL_SELECT_mind" type="select" label="Set Mind" help="Exclude variants (--geno) and/or samples (--mind) with missing call frequencies greater than a threshold (default 0.1). (Note that the default threshold is only applied if --geno/--mind is invoked without a parameter; when --geno/--mind is not invoked, no missing call frequency ceiling is enforced at all. Other inclusion/exclusion default thresholds work the same way.) By default, when a dosage is present but a hardcall is not, the genotype is treated as missing; add the 'dosage' modifier to treat this case as nonmissing. Alternatively, you can use 'hh-missing' to also treat heterozygous haploid calls as missing." argument="--mind"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="mind_MOD_0_0" type="text" label="val" value="" optional="False" argument="val" help=""/> + <conditional name="CONDITIONAL_mind_MOD_1"> + <param name="CONDITIONAL_SELECT_mind_MOD_1" type="select" label="How to set Mind"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="mind_MOD_1" type="select" label="Select value"> + <option value="{dosage">{dosage</option> +<option value="hh-missing}">hh-missing}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_require_pheno"> + <param name="CONDITIONAL_SELECT_require_pheno" type="select" label="Set Require pheno" help="Remove samples missing any of the named " argument="--require-pheno"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="require_pheno_MOD_0_0" type="text" label="name(s)..." value="" optional="False" argument="name(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_require_covar"> + <param name="CONDITIONAL_SELECT_require_covar" type="select" label="Set Require covar" help="" argument="--require-covar"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="require_covar_MOD_0_0" type="text" label="name(s)..." value="" optional="False" argument="name(s)..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_maf"> + <param name="CONDITIONAL_SELECT_maf" type="select" label="Set Maf" help="Exclude variants with allele frequency lower than a (alias: --min-af) threshold (default 0.01). By default, the nonmajor allele frequency is used; the other supported modes are 'nref' (non-reference), 'alt1', and 'minor' (least frequent). bcftools freq:mode notation is permitted." argument="--maf"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="maf_MOD_0_0" type="float" label="freq" value="" optional="False" argument="freq" help=""/> + <param name="maf_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_max_maf"> + <param name="CONDITIONAL_SELECT_max_maf" type="select" label="Set Max maf" help="Exclude variants with MAF greater than the (alias: --max-af) threshold." argument="--max-maf"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="max_maf_MOD_0_0" type="float" label="freq" value="" optional="True" argument="freq" help=""/> + <param name="max_maf_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_mac"> + <param name="CONDITIONAL_SELECT_mac" type="select" label="Set Mac" help="Exclude variants with allele dosage lower than the (alias: --min-ac) given threshold." argument="--mac"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="mac_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/> + <param name="mac_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_max_mac"> + <param name="CONDITIONAL_SELECT_max_mac" type="select" label="Set Max mac" help="Exclude variants with allele dosage greater than (alias: --max-ac) the given threshold." argument="--max-mac"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="max_mac_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/> + <param name="max_mac_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_maf_succ"> + <param name="CONDITIONAL_SELECT_maf_succ" type="select" label="Set Maf succ" help="Rule of succession allele frequency estimation (used in EIGENSOFT). Given j observations of one allele and k observations of the other for a biallelic variant, infer allele frequencies of (j+1) / (j+k+2) and (k+1) / (j+k+2), rather than the default j / (j+k) and k / (j+k). Note that this does not affect --freq's output. " argument="--maf-succ"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_min_alleles"> + <param name="CONDITIONAL_SELECT_min_alleles" type="select" label="Set Min alleles" help="Exclude variants with fewer than the given # of alleles. (When a variant has exactly one ALT allele, and it's a missing-code, it's excluded by "--min-alleles 2".) " argument="--min-alleles"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="min_alleles_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_max_alleles"> + <param name="CONDITIONAL_SELECT_max_alleles" type="select" label="Set Max alleles" help="Exclude variants with more than the given # of alleles. " argument="--max-alleles"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="max_alleles_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_read_freq"> + <param name="CONDITIONAL_SELECT_read_freq" type="select" label="Set Read freq" help="Load allele frequency estimates from the given --freq or --geno-counts (or PLINK 1.9 --freqx) report, instead of imputing them from the immediate dataset. " argument="--read-freq"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="read_freq_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_hwe"> + <param name="CONDITIONAL_SELECT_hwe" type="select" label="Set Hwe" help="Exclude variants with Hardy-Weinberg equilibrium exact test p-values below a threshold. * By default, only founders are considered. * chrX p-values are now computed using Graffelman and Weir's method. * For variants with k alleles with k>2, k separate 'biallelic' tests are performed, and the variant is filtered out if any of them fail. * With 'keep-fewhet', variants which fail the test in the too-few-hets direction are not excluded. On chrX, this uses the ratio between the Graffelman/Weir p-value and the female-only p-value. * There is currently no special handling of case/control phenotypes." argument="--hwe"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="hwe_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/> + <param name="hwe_MOD_1_0" type="text" label="'midp'" value="" optional="False" argument="'midp'" help=""/> + <param name="hwe_MOD_2_0" type="text" label="'keep-fewhet'" value="" optional="False" argument="'keep-fewhet'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_mach_r2_filter"> + <param name="CONDITIONAL_SELECT_mach_r2_filter" type="select" label="Set Mach r2 filter" help="Exclude variants with MaCH imputation quality metric less than min or greater than max (defaults 0.1 and 2.0). (Monomorphic variants, with r2 = nan, are not excluded.) * This is NOT identical to the R2 metric reported by Minimac3 0.1.13+; see below. * If a single parameter is provided, it is treated as the minimum. * The metric is not computed on chrX and MT. " argument="--mach-r2-filter"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="mach_r2_filter_MOD_0_0" type="text" label="min" value="" optional="False" argument="min" help=""/> + <param name="mach_r2_filter_MOD_1_0" type="text" label="max" value="" optional="False" argument="max" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_minimac3_r2_filter"> + <param name="CONDITIONAL_SELECT_minimac3_r2_filter" type="select" label="Set Minimac3 r2 filter" help="Compute Minimac3 R2 values from scratch, and exclude variants with R2 less than min or (if max is provided) greater than max. * Note that this requires phased-dosage data for all samples and variants; otherwise this will systematically underestimate imputation quality, since unphased hardcalls/dosages are treated as if they were maximally uncertain. (Use --extract-if-info/--exclude-if-info to filter on precomputed Minimac3 R2 in a VCF/.pvar INFO column.) " argument="--minimac3-r2-filter"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="minimac3_r2_filter_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/> + <param name="minimac3_r2_filter_MOD_1_0" type="text" label="max" value="" optional="False" argument="max" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_keep_females"> + <param name="CONDITIONAL_SELECT_keep_females" type="select" label="Set Keep females" help="Exclude male and unknown-sex samples. " argument="--keep-females"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_keep_males"> + <param name="CONDITIONAL_SELECT_keep_males" type="select" label="Set Keep males" help="Exclude female and unknown-sex samples. " argument="--keep-males"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_keep_nosex"> + <param name="CONDITIONAL_SELECT_keep_nosex" type="select" label="Set Keep nosex" help="Exclude all known-sex samples. " argument="--keep-nosex"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_remove_females"> + <param name="CONDITIONAL_SELECT_remove_females" type="select" label="Set Remove females" help="Exclude female samples. " argument="--remove-females"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_remove_males"> + <param name="CONDITIONAL_SELECT_remove_males" type="select" label="Set Remove males" help="Exclude male samples. " argument="--remove-males"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_remove_nosex"> + <param name="CONDITIONAL_SELECT_remove_nosex" type="select" label="Set Remove nosex" help="Exclude unknown-sex samples. " argument="--remove-nosex"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_keep_founders"> + <param name="CONDITIONAL_SELECT_keep_founders" type="select" label="Set Keep founders" help="Exclude nonfounder samples. " argument="--keep-founders"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_keep_nonfounders"> + <param name="CONDITIONAL_SELECT_keep_nonfounders" type="select" label="Set Keep nonfounders" help="Exclude founder samples. " argument="--keep-nonfounders"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_keep_if"> + <param name="CONDITIONAL_SELECT_keep_if" type="select" label="Set Keep if" help="Exclude samples which don't/do satisfy a " argument="--keep-if"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="keep_if_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/> + <param name="keep_if_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/> + <param name="keep_if_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_remove_if"> + <param name="CONDITIONAL_SELECT_remove_if" type="select" label="Set Remove if" help="" argument="--remove-if"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="remove_if_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/> + <param name="remove_if_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/> + <param name="remove_if_MOD_2_0" type="text" label="v" value="" optional="True" argument="v" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_nonfounders"> + <param name="CONDITIONAL_SELECT_nonfounders" type="select" label="Set Nonfounders" help="Include nonfounders in allele freq/HWE calculations. " argument="--nonfounders"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_bad_freqs"> + <param name="CONDITIONAL_SELECT_bad_freqs" type="select" label="Set Bad freqs" help="When PLINK 2 needs decent allele frequencies, it normally errors out if they aren't provided by --read-freq and less than 50 founders are available to impute them from. Use --bad-freqs to force PLINK 2 to proceed in this case. " argument="--bad-freqs"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_export_allele"> + <param name="CONDITIONAL_SELECT_export_allele" type="select" label="Set Export allele" help="With --export A/A-transpose/AD, count alleles named in the file, instead of REF alleles. " argument="--export-allele"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="export_allele_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_output_chr"> + <param name="CONDITIONAL_SELECT_output_chr" type="select" label="Set Output chr" help="Set chromosome coding scheme in output files by providing the desired human mitochondrial code. Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM', and 'chrMT'; default is now 'MT' (note that this is a change from PLINK 1.x, which defaulted to '26'). " argument="--output-chr"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="output_chr_MOD_0_0" type="text" label="MT code" value="" optional="True" argument="MT code" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_output_missing_genotype"> + <param name="CONDITIONAL_SELECT_output_missing_genotype" type="select" label="Set Output missing genotype" help="Set the code used to represent missing genotypes in output files (default '.'). " argument="--output-missing-genotype"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="output_missing_genotype_MOD_0_0" type="text" label="ch" value="" optional="True" argument="ch" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_output_missing_phenotype"> + <param name="CONDITIONAL_SELECT_output_missing_phenotype" type="select" label="Set Output missing phenotype" help="Set the string used to represent missing phenotypes in output files (default 'NA'). " argument="--output-missing-phenotype"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="output_missing_phenotype_MOD_0_0" type="text" label="s" value="" optional="True" argument="s" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_sort_vars"> + <param name="CONDITIONAL_SELECT_sort_vars" type="select" label="Set Sort vars" help="Sort variants by chromosome, then position, then ID. The following string orders are supported: * 'natural'/'n': Natural sort (default). * 'ascii'/'a': ASCII. This must be used with --make-[b]pgen/--make-bed. " argument="--sort-vars"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="sort_vars_MOD_0_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_set_hh_missing"> + <param name="CONDITIONAL_SELECT_set_hh_missing" type="select" label="Set Set hh missing" help="Make --make-[b]pgen/--make-bed set non-MT heterozygous haploid hardcalls, and all female chrY calls, to missing. (Unlike PLINK 1.x, this treats unknown-sex chrY genotypes like males, not females.) By default, all associated dosages are also erased; use 'keep-dosage' to keep them all. " argument="--set-hh-missing"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="set_hh_missing_MOD_0_0" type="text" label="'keep-dosage'" value="" optional="False" argument="'keep-dosage'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_set_mixed_mt_missing"> + <param name="CONDITIONAL_SELECT_set_mixed_mt_missing" type="select" label="Set Set mixed mt missing" help="Make --make-[b]pgen/--make-bed set mixed MT hardcalls to missing. " argument="--set-mixed-mt-missing"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="set_mixed_mt_missing_MOD_0_0" type="text" label="'keep-dosage'" value="" optional="False" argument="'keep-dosage'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_OVERLOADED_split_par"> + <param name="CONDITIONAL_OVERLOADED_SELECT_split_par" type="select" label="Choose argument form for Split_par" help="Overloaded argument, must chose a form"> + <option value="form_0">Form 0</option> + <option value="form_1">Form 1</option> + </param> + <when value="form_0"> + + <conditional name="CONDITIONAL_split_par"> + <param name="CONDITIONAL_SELECT_split_par" type="select" label="Set Split par" help="Changes chromosome code of all X chromosome " argument="--split-par"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="split_par_MOD_0_0" type="text" label="bp1" value="" optional="True" argument="bp1" help=""/> + <param name="split_par_MOD_1_0" type="text" label="bp2" value="" optional="True" argument="bp2" help=""/> + </when> + </conditional> + </when> + <when value="form_1"> + + <conditional name="CONDITIONAL_split_par"> + <param name="CONDITIONAL_SELECT_split_par" type="select" label="Set Split par" help="* 'b36'/'hg18' = NCBI 36, 2709521/154584237 * 'b37'/'hg19' = GRCh37, 2699520/154931044 * 'b38'/'hg38' = GRCh38, 2781479/155701383 " argument="--split-par"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="split_par_MOD_0_0" type="text" label="build" value="" optional="True" argument="build" help=""/> + <param name="split_par_MOD_1_0" type="text" label="= bp1 to PAR1, and those with position" value="" optional="True" argument="= bp1 to PAR1, and those with position" help=""/> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_merge_par"> + <param name="CONDITIONAL_SELECT_merge_par" type="select" label="Set Merge par" help='Merge PAR1/PAR2 back with X. Requires PAR1 to be positioned immediately before X, and PAR2 to be immediately after X. (Should *not* be used with "--export vcf", since it causes male homozygous/missing calls in PAR1/PAR2 to be reported as haploid.) ' argument="--merge-par"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_merge_x"> + <param name="CONDITIONAL_SELECT_merge_x" type="select" label="Set Merge x" help="Merge XY back with X. This usually has to be combined with --sort-vars. " argument="--merge-x"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_set_missing_var_ids"> + <param name="CONDITIONAL_SELECT_set_missing_var_ids" type="select" label="Set Set missing var ids" help="Given a template string with a '@' where the " argument="--set-missing-var-ids"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="set_missing_var_ids_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_set_all_var_ids"> + <param name="CONDITIONAL_SELECT_set_all_var_ids" type="select" label="Set Set all var ids" help="" argument="--set-all-var-ids"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="set_all_var_ids_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_var_id_multi"> + <param name="CONDITIONAL_SELECT_var_id_multi" type="select" label="Set Var id multi" help="Specify alternative templates for multiallelic " argument="--var-id-multi"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="var_id_multi_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_var_id_multi_nonsnp"> + <param name="CONDITIONAL_SELECT_var_id_multi_nonsnp" type="select" label="Set Var id multi nonsnp" help="" argument="--var-id-multi-nonsnp"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="var_id_multi_nonsnp_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_new_id_max_allele_len"> + <param name="CONDITIONAL_SELECT_new_id_max_allele_len" type="select" label="Set New id max allele len" help="Specify maximum number of leading characters from allele codes to include in new variant IDs, and behavior on longer codes (defaults 23, error)." argument="--new-id-max-allele-len"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="new_id_max_allele_len_MOD_0_0" type="text" label="len" value="" optional="True" argument="len" help=""/> + <conditional name="CONDITIONAL_new_id_max_allele_len_MOD_1"> + <param name="CONDITIONAL_SELECT_new_id_max_allele_len_MOD_1" type="select" label="How to set New id max allele len"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="new_id_max_allele_len_MOD_1" type="select" label="Select value"> + <option value="{error">{error</option> +<option value="missing">missing</option> +<option value="truncate}">truncate}</option> +</param> + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_missing_var_code"> + <param name="CONDITIONAL_SELECT_missing_var_code" type="select" label="Set Missing var code" help="Change unnamed variant code for --rm-dup, --set-{missing|all}-var-ids, and --recover-var-ids (default '.'). " argument="--missing-var-code"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="missing_var_code_MOD_0_0" type="text" label="str" value="" optional="True" argument="str" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_update_map"> + <param name="CONDITIONAL_SELECT_update_map" type="select" label="Set Update map" help="Update variant bp positions. " argument="--update-map"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="update_map_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/> + <param name="update_map_MOD_1_0" type="text" label="bpcol" value="" optional="False" argument="bpcol" help=""/> + <param name="update_map_MOD_2_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/> + <param name="update_map_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_update_name"> + <param name="CONDITIONAL_SELECT_update_name" type="select" label="Set Update name" help="Update variant IDs. " argument="--update-name"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="update_name_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/> + <param name="update_name_MOD_1_0" type="text" label="newcol" value="" optional="False" argument="newcol" help=""/> + <param name="update_name_MOD_2_0" type="text" label="oldcol" value="" optional="False" argument="oldcol" help=""/> + <param name="update_name_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_recover_var_ids"> + <param name="CONDITIONAL_SELECT_recover_var_ids" type="select" label="Set Recover var ids" help="Undo --set-all-var-ids, given the original .pvar/VCF/.bim file. Original IDs are looked up by position and allele codes. * By default, if the original-ID file is a .bim, allele order is ignored. Use 'strict-bim-order' to force A1=ALT, A2=REF. * If any variant has multiple matching records in the original-ID file, and the IDs conflict, --recover-var-ids writes the affected (current) ID(s) to <output prefix>.recoverid.dup, and normally errors out. If the original-ID file has the same number of variants in the same order, you can still recover the old IDs with the 'rigid' modifier in this case. Alternatively, to proceed and assign the missing-ID code to these variants, add the 'force' modifier. (The .recoverid.dup file is still written when 'rigid' or 'force' is specified.) * --recover-var-ids normally expects to replace all variant IDs, and errors out if any are left untouched. Add the 'partial' modifier when you actually want to update just a proper subset." argument="--recover-var-ids"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="recover_var_ids_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/> + <param name="recover_var_ids_MOD_1_0" type="text" label="'strict-bim-order'" value="" optional="False" argument="'strict-bim-order'" help=""/> + <conditional name="CONDITIONAL_recover_var_ids_MOD_2"> + <param name="CONDITIONAL_SELECT_recover_var_ids_MOD_2" type="select" label="How to set Recover var ids"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="recover_var_ids_MOD_2" type="select" label="Select value"> + <option value="{rigid">{rigid</option> +<option value="force}">force}</option> +</param> + </when> + </conditional> + <param name="recover_var_ids_MOD_3_0" type="text" label="'partial'" value="" optional="False" argument="'partial'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_update_alleles"> + <param name="CONDITIONAL_SELECT_update_alleles" type="select" label="Set Update alleles" help="Update variant allele codes. " argument="--update-alleles"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="update_alleles_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/> + </when> + </conditional> + <conditional name="CONDITIONAL_update_ids"> + <param name="CONDITIONAL_SELECT_update_ids" type="select" label="Set Update ids" help="Update sample IDs. " argument="--update-ids"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="update_ids_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/> + </when> + </conditional> + <conditional name="CONDITIONAL_update_parents"> + <param name="CONDITIONAL_SELECT_update_parents" type="select" label="Set Update parents" help="Update parental IDs. " argument="--update-parents"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="update_parents_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/> + </when> + </conditional> + <conditional name="CONDITIONAL_update_sex"> + <param name="CONDITIONAL_SELECT_update_sex" type="select" label="Set Update sex" help="Update sex information. * By default, if there is a header line starting with '#FID'/'#IID', sex is loaded from the first column titled 'SEX' (any capitalization); otherwise, column 3 is assumed. Use 'col-num=' to force a column number. * Only the first character in the sex column is processed. By default, '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female, and '0'/'N' is interpreted as unknown-sex. To change this to '0'/'M'/'m' = male, '1'/'F'/'f' = female, anything else other than '2' = unknown-sex, add 'male0'." argument="--update-sex"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="update_sex_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="update_sex_MOD_1_0" type="text" label="'col-num='<n>" value="" optional="False" argument="'col-num='<n>" help=""/> + <param name="update_sex_MOD_2_0" type="text" label="'male0'" value="" optional="False" argument="'male0'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_real_ref_alleles"> + <param name="CONDITIONAL_SELECT_real_ref_alleles" type="select" label="Set Real ref alleles" help="Treat A2 alleles in a PLINK 1.x fileset as actual REF alleles; otherwise they're marked as provisional. " argument="--real-ref-alleles"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_maj_ref"> + <param name="CONDITIONAL_SELECT_maj_ref" type="select" label="Set Maj ref" help="Set major alleles to reference, like PLINK 1.x automatically did. (Note that this is now opt-in rather than opt-out; --keep-allele-order is no longer necessary to prevent allele-swapping.) * This can only be used in runs with --make-bed/--make-[b]pgen/--export and no other commands. * By default, this only affects variants marked as having 'provisional' reference alleles. Add 'force' to apply this to all variants. * All new reference alleles are marked as provisional. " argument="--maj-ref"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="maj_ref_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_ref_allele"> + <param name="CONDITIONAL_SELECT_ref_allele" type="select" label="Set Ref allele" help="" argument="--ref-allele"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="ref_allele_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/> + <param name="ref_allele_MOD_1_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="ref_allele_MOD_2_0" type="text" label="refcol" value="" optional="False" argument="refcol" help=""/> + <param name="ref_allele_MOD_3_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/> + <param name="ref_allele_MOD_4_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_alt1_allele"> + <param name="CONDITIONAL_SELECT_alt1_allele" type="select" label="Set Alt1 allele" help="These set the alleles specified in the file to ref (--ref-allele) or alt1 (--alt1-allele). They can be combined in the same run. * These can only be used in runs with --make-bed/--make-[b]pgen/--export and no other commands. * "--ref-allele <VCF filename> 4 3 '#'", which scrapes reference allele assignments from a VCF file, is especially useful. * By default, these error out when asked to change a 'known' reference allele. Add 'force' to permit that (when e.g. switching to a new reference genome). * When --alt1-allele changes the previous ref allele to alt1, the previous alt1 allele is set to reference and marked as provisional." argument="--alt1-allele"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="alt1_allele_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/> + <param name="alt1_allele_MOD_1_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/> + <param name="alt1_allele_MOD_2_0" type="text" label="alt1col" value="" optional="False" argument="alt1col" help=""/> + <param name="alt1_allele_MOD_3_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/> + <param name="alt1_allele_MOD_4_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_ref_from_fa"> + <param name="CONDITIONAL_SELECT_ref_from_fa" type="select" label="Set Ref from fa" help="This sets reference alleles from the --fa file when it can be done unambiguously (note that it's never possible for deletions or some insertions). By default, it errors out when asked to change a 'known' reference allele; add the 'force' modifier to permit that. " argument="--ref-from-fa"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="ref_from_fa_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_normalize"> + <param name="CONDITIONAL_SELECT_normalize" type="select" label="Set Normalize" help="Left-normalize all variants, using the --fa file. (alias: --norm) (Assumes no differences in capitalization.) The 'list' modifier causes a list of affected variant IDs to be written to <output prefix>.normalized." argument="--normalize"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="normalize_MOD_0_0" type="text" label="'list'" value="" optional="False" argument="'list'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_indiv_sort"> + <param name="CONDITIONAL_SELECT_indiv_sort" type="select" label="Set Indiv sort" help="Specify sample ID sort order for merge and --make-[b]pgen/--make-bed. The following four modes are supported: * 'none'/'0' keeps samples in the order they were loaded. Default for non-merge. * 'natural'/'n' invokes "natural sort", e.g. 'id2' < 'ID3' < 'id10'. Default when merging. * 'ascii'/'a' sorts in ASCII order, e.g. 'ID3' < 'id10' < 'id2'. * 'file'/'f' uses the order in the given file (named in the last parameter). " argument="--indiv-sort"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="indiv_sort_MOD_0_0" type="text" label="mode" value="" optional="True" argument="mode" help=""/> + <param name="indiv_sort_MOD_1_0" type="data" format="txt" label="f" multiple="False" optional="False" argument="f"/> + </when> + </conditional> + <conditional name="CONDITIONAL_king_table_filter"> + <param name="CONDITIONAL_SELECT_king_table_filter" type="select" label="Set King table filter" help="Specify minimum kinship coefficient for inclusion in --make-king-table report. " argument="--king-table-filter"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="king_table_filter_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_king_table_subset"> + <param name="CONDITIONAL_SELECT_king_table_subset" type="select" label="Set King table subset" help="Restrict current --make-king-table run to sample pairs listed in the given .kin0 file. If a second parameter is provided, only sample pairs with kinship >= that threshold (in the input .kin0) are processed. " argument="--king-table-subset"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="king_table_subset_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/> + <param name="king_table_subset_MOD_1_0" type="text" label="kmin" value="" optional="False" argument="kmin" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_condition"> + <param name="CONDITIONAL_SELECT_condition" type="select" label="Set Condition" help="" argument="--condition"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="condition_MOD_0_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/> + <conditional name="CONDITIONAL_condition_MOD_1"> + <param name="CONDITIONAL_SELECT_condition_MOD_1" type="select" label="How to set Condition"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="condition_MOD_1" type="select" label="Select value"> + <option value="{dominant">{dominant</option> +<option value="recessive}">recessive}</option> +</param> + </when> + </conditional> + <param name="condition_MOD_2_0" type="text" label="'multiallelic'" value="" optional="False" argument="'multiallelic'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_condition_list"> + <param name="CONDITIONAL_SELECT_condition_list" type="select" label="Set Condition list" help="Add the given variant, or all variants in the given file, as --glm covariates. By default, this errors out if any of the variants are multiallelic; add the 'multiallelic' ('m' for short) modifier to allow them. They'll effectively be split against the major allele (unless --glm's 'omit-ref' modifier was specified), and all induced covariate names--even for biallelic variants--will have an underscore followed by the allele code at the end." argument="--condition-list"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="condition_list_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/> + <conditional name="CONDITIONAL_condition_list_MOD_1"> + <param name="CONDITIONAL_SELECT_condition_list_MOD_1" type="select" label="How to set Condition list"> + <option value="no_set" selected="True">Don't set</option> + <option value="from_list">Select from list</option> + + </param> + <when value="no_set"> + </when> + + <when value="from_list"> + <param name="condition_list_MOD_1" type="select" label="Select value"> + <option value="{dominant">{dominant</option> +<option value="recessive}">recessive}</option> +</param> + </when> + </conditional> + <param name="condition_list_MOD_2_0" type="text" label="'multiallelic'" value="" optional="False" argument="'multiallelic'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_parameters"> + <param name="CONDITIONAL_SELECT_parameters" type="select" label="Set Parameters" help="Include only the given covariates/interactions in the --glm model, identified by a list of 1-based indices and/or ranges of them. " argument="--parameters"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="parameters_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_OVERLOADED_tests"> + <param name="CONDITIONAL_OVERLOADED_SELECT_tests" type="select" label="Choose argument form for Tests" help="Overloaded argument, must chose a form"> + <option value="form_0">Form 0</option> + <option value="form_1">Form 1</option> + </param> + <when value="form_0"> + + <conditional name="CONDITIONAL_tests"> + <param name="CONDITIONAL_SELECT_tests" type="select" label="Set Tests" help="Perform a (joint) test on the specified term(s) in the " argument="--tests"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="tests_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + </when> + <when value="form_1"> + + <conditional name="CONDITIONAL_tests"> + <param name="CONDITIONAL_SELECT_tests" type="select" label="Set Tests" help="" argument="--tests"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + </when> + </conditional> + <conditional name="CONDITIONAL_vif"> + <param name="CONDITIONAL_SELECT_vif" type="select" label="Set Vif" help="Set VIF threshold for --glm multicollinearity check (default 50). (This is no longer skipped for case/control phenotypes.) " argument="--vif"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vif_MOD_0_0" type="text" label="max VIF" value="" optional="True" argument="max VIF" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_max_corr"> + <param name="CONDITIONAL_SELECT_max_corr" type="select" label="Set Max corr" help="Skip --glm regression when the absolute value of the correlation between two predictors exceeds this value (default 0.999). " argument="--max-corr"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="max_corr_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_xchr_model"> + <param name="CONDITIONAL_SELECT_xchr_model" type="select" label="Set Xchr model" help="Set the chrX --glm/--condition[-list]/--[v]score model. * '0' = skip chrX. * '1' = add sex as a covar on chrX, code males 0..1. * '2' (default) = chrX sex covar, code males 0..2. (Use the --glm 'interaction' modifier to test for interaction between genotype and sex.) " argument="--xchr-model"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="xchr_model_MOD_0_0" type="text" label="m" value="" optional="True" argument="m" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust"> + <param name="CONDITIONAL_SELECT_adjust" type="select" label="Set Adjust" help="For each association test in this run, report some basic multiple-testing corrections, sorted in increasing-p-value order. Modifiers work the same way as they do on --adjust-file." argument="--adjust"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/> + <param name="adjust_MOD_1_0" type="text" label="'gc'" value="" optional="False" argument="'gc'" help=""/> + <param name="adjust_MOD_2_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/> + <param name="adjust_MOD_3_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_lambda"> + <param name="CONDITIONAL_SELECT_lambda" type="select" label="Set Lambda" help="Set genomic control lambda for --adjust[-file]. " argument="--lambda"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_chr_field"> + <param name="CONDITIONAL_SELECT_adjust_chr_field" type="select" label="Set Adjust chr field" help="Set --adjust-file input field names. When " argument="--adjust-chr-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_chr_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_pos_field"> + <param name="CONDITIONAL_SELECT_adjust_pos_field" type="select" label="Set Adjust pos field" help="" argument="--adjust-pos-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_pos_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_id_field"> + <param name="CONDITIONAL_SELECT_adjust_id_field" type="select" label="Set Adjust id field" help="" argument="--adjust-id-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_id_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_ref_field"> + <param name="CONDITIONAL_SELECT_adjust_ref_field" type="select" label="Set Adjust ref field" help="" argument="--adjust-ref-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_ref_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_alt_field"> + <param name="CONDITIONAL_SELECT_adjust_alt_field" type="select" label="Set Adjust alt field" help="" argument="--adjust-alt-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_alt_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_a1_field"> + <param name="CONDITIONAL_SELECT_adjust_a1_field" type="select" label="Set Adjust a1 field" help="" argument="--adjust-a1-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_a1_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_test_field"> + <param name="CONDITIONAL_SELECT_adjust_test_field" type="select" label="Set Adjust test field" help="" argument="--adjust-test-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_test_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_adjust_p_field"> + <param name="CONDITIONAL_SELECT_adjust_p_field" type="select" label="Set Adjust p field" help="" argument="--adjust-p-field"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="adjust_p_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_ci"> + <param name="CONDITIONAL_SELECT_ci" type="select" label="Set Ci" help="Report confidence ratios for odds ratios/betas. " argument="--ci"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="ci_MOD_0_0" type="text" label="size" value="" optional="True" argument="size" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_pfilter"> + <param name="CONDITIONAL_SELECT_pfilter" type="select" label="Set Pfilter" help="Filter out assoc. test results with higher p-values. " argument="--pfilter"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="pfilter_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_score_col_nums"> + <param name="CONDITIONAL_SELECT_score_col_nums" type="select" label="Set Score col nums" help="Process all the specified coefficient columns in the --score file, identified by 1-based indexes and/or ranges of them. " argument="--score-col-nums"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="score_col_nums_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_q_score_range"> + <param name="CONDITIONAL_SELECT_q_score_range" type="select" label="Set Q score range" help="Apply --score to subset(s) of variants in the primary score list(s) based on e.g. p-value ranges. * The first file should have range labels in the first column, p-value lower bounds in the second column, and upper bounds in the third column. Lines with too few entries, or nonnumeric values in the second or third column, are ignored. * The second file should contain a variant ID and a p-value on each line (except possibly the first). Variant IDs are read from column #i and p-values are read from column #j, where i defaults to 1 and j defaults to i+1. The 'header' modifier causes the first nonempty line of this file to be skipped. * By default, --q-score-range errors out when a variant ID appears multiple times in the data file (and is also present in the main dataset). To use the minimum p-value in this case instead, add the 'min' modifier." argument="--q-score-range"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="q_score_range_MOD_0_0" type="text" label="range file" value="" optional="True" argument="range file" help=""/> + <param name="q_score_range_MOD_1_0" type="text" label="data file" value="" optional="True" argument="data file" help=""/> + <param name="q_score_range_MOD_2_0" type="text" label="i" value="" optional="False" argument="i" help=""/> + <param name="q_score_range_MOD_3_0" type="text" label="j" value="" optional="False" argument="j" help=""/> + <param name="q_score_range_MOD_4_0" type="text" label="'header'" value="" optional="False" argument="'header'" help=""/> + <param name="q_score_range_MOD_5_0" type="text" label="'min'" value="" optional="False" argument="'min'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_vscore_col_nums"> + <param name="CONDITIONAL_SELECT_vscore_col_nums" type="select" label="Set Vscore col nums" help="Process all the specified coefficient columns in the --variant-score file, identified by 1-based indexes and/or ranges of them. " argument="--vscore-col-nums"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="vscore_col_nums_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_memory"> + <param name="CONDITIONAL_SELECT_memory" type="select" label="Set Memory" help="Set size, in MiB, of initial workspace malloc attempt. To error out instead of reducing the request size when the initial attempt fails, add the 'require' modifier. " argument="--memory"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="memory_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + <param name="memory_MOD_1_0" type="text" label="'require'" value="" optional="False" argument="'require'" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_threads"> + <param name="CONDITIONAL_SELECT_threads" type="select" label="Set Threads" help="Set maximum number of compute threads. " argument="--threads"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="threads_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_d"> + <param name="CONDITIONAL_SELECT_d" type="select" label="Set D" help="Change variant/covariate range delimiter (normally '-'). " argument="--d"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="d_MOD_0_0" type="text" label="char" value="" optional="True" argument="char" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_seed"> + <param name="CONDITIONAL_SELECT_seed" type="select" label="Set Seed" help='Set random number seed(s). Each value must be an integer between 0 and 4294967295 inclusive. Note that --threads and "--memory require" may also be needed to reproduce some randomized runs. ' argument="--seed"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="seed_MOD_0_0" type="text" label="val..." value="" optional="True" argument="val..." help="Multiple values are allowed"/> + </when> + </conditional> + <conditional name="CONDITIONAL_output_min_p"> + <param name="CONDITIONAL_SELECT_output_min_p" type="select" label="Set Output min p" help="Specify minimum p-value to write to reports. (2.23e-308 is useful for preventing underflow in some programs.) " argument="--output-min-p"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="output_min_p_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/> + </when> + </conditional> + <conditional name="CONDITIONAL_debug"> + <param name="CONDITIONAL_SELECT_debug" type="select" label="Set Debug" help="Use slower, more crash-resistant logging method. " argument="--debug"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_randmem"> + <param name="CONDITIONAL_SELECT_randmem" type="select" label="Set Randmem" help="Randomize initial workspace memory (helps catch uninitialized-memory bugs). " argument="--randmem"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_warning_errcode"> + <param name="CONDITIONAL_SELECT_warning_errcode" type="select" label="Set Warning errcode" help="Return a nonzero error code to the OS when a run completes with warning(s). " argument="--warning-errcode"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + </when> + </conditional> + <conditional name="CONDITIONAL_zst_level"> + <param name="CONDITIONAL_SELECT_zst_level" type="select" label="Set Zst level" help="Set the Zstd compression level (1-22, default 3). " argument="--zst-level"> + <option value="no_set" selected="True">Don't set</option> + <option value="set">Set value(s)</option> + </param> + <when value="no_set"> + </when> + <when value="set"> + + <param name="zst_level_MOD_0_0" type="text" label="lvl" value="" optional="True" argument="lvl" help=""/> + </when> + </conditional> + </inputs> + <outputs> + <data name="OUTPUT_plink_acount __freq" format="plink.acount --freq" label="${tool.name} on ${on_string}: plink.acount --freq" from_work_dir="plink.acount --freq" hidden="True"/> + <data name="OUTPUT_plink_adjusted __adjust_" format="plink.adjusted --adjust," label="${tool.name} on ${on_string}: plink.adjusted --adjust," from_work_dir="plink.adjusted --adjust," hidden="True"/> + <data name="OUTPUT_plink_afreq __freq Allele" format="plink.afreq --freq Allele" label="${tool.name} on ${on_string}: plink.afreq --freq Allele" from_work_dir="plink.afreq --freq Allele" hidden="True"/> + <data name="OUTPUT_plink_bcf __export" format="plink.bcf --export" label="${tool.name} on ${on_string}: plink.bcf --export" from_work_dir="plink.bcf --export" hidden="True"/> + <data name="OUTPUT_plink_bed __make_bed___ PLINK" format="plink.bed --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.bed --make-bed... PLINK" from_work_dir="plink.bed --make-bed... PLINK" hidden="True"/> + <data name="OUTPUT_plink_bgen __export" format="plink.bgen --export" label="${tool.name} on ${on_string}: plink.bgen --export" from_work_dir="plink.bgen --export" hidden="True"/> + <data name="OUTPUT_plink_bim __make_bed___ PLINK" format="plink.bim --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.bim --make-bed... PLINK" from_work_dir="plink.bim --make-bed... PLINK" hidden="True"/> + <data name="OUTPUT_plink_bin several Matrix" format="plink.bin several Matrix" label="${tool.name} on ${on_string}: plink.bin several Matrix" from_work_dir="plink.bin several Matrix" hidden="True"/> + <data name="OUTPUT_plink_bins __freq" format="plink.bins --freq" label="${tool.name} on ${on_string}: plink.bins --freq" from_work_dir="plink.bins --freq" hidden="True"/> + <data name="OUTPUT_plink_cov __write_covar___ Covariate" format="plink.cov --write-covar... Covariate" label="${tool.name} on ${on_string}: plink.cov --write-covar... Covariate" from_work_dir="plink.cov --write-covar... Covariate" hidden="True"/> + <data name="OUTPUT_plink_eigenval __pca Principal" format="plink.eigenval --pca Principal" label="${tool.name} on ${on_string}: plink.eigenval --pca Principal" from_work_dir="plink.eigenval --pca Principal" hidden="True"/> + <collection name="OUTPUT_plink_eigenvec_ __pca Principal" type="list" label="plink.eigenvec*	--pca	Principal" hidden="True"> + <discover_datasets pattern="plink\.eigenvec(?P<name>)\	\-\-pca\	Principal" format="plink.eigenvec* --pca Principal"/> + </collection> + <data name="OUTPUT_plink_fam __make_bed___ PLINK" format="plink.fam --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.fam --make-bed... PLINK" from_work_dir="plink.fam --make-bed... PLINK" hidden="True"/> + <data name="OUTPUT_plink_fst_summary __fst Between_population" format="plink.fst.summary --fst Between-population" label="${tool.name} on ${on_string}: plink.fst.summary --fst Between-population" from_work_dir="plink.fst.summary --fst Between-population" hidden="True"/> + <data name="OUTPUT_plink_fst_var __fst Per_variant" format="plink.fst.var --fst Per-variant" label="${tool.name} on ${on_string}: plink.fst.var --fst Per-variant" from_work_dir="plink.fst.var --fst Per-variant" hidden="True"/> + <data name="OUTPUT_plink_gcount __geno_counts Genotype" format="plink.gcount --geno-counts Genotype" label="${tool.name} on ${on_string}: plink.gcount --geno-counts Genotype" from_work_dir="plink.gcount --geno-counts Genotype" hidden="True"/> + <data name="OUTPUT_plink_gen __export" format="plink.gen --export" label="${tool.name} on ${on_string}: plink.gen --export" from_work_dir="plink.gen --export" hidden="True"/> + <data name="OUTPUT_plink_glm_firth __glm" format="plink.glm.firth --glm" label="${tool.name} on ${on_string}: plink.glm.firth --glm" from_work_dir="plink.glm.firth --glm" hidden="True"/> + <data name="OUTPUT_plink_glm_logistic __glm" format="plink.glm.logistic --glm" label="${tool.name} on ${on_string}: plink.glm.logistic --glm" from_work_dir="plink.glm.logistic --glm" hidden="True"/> + <data name="OUTPUT_plink_glm_logistic_hybrid __glm Logistic/Firth" format="plink.glm.logistic.hybrid --glm Logistic/Firth" label="${tool.name} on ${on_string}: plink.glm.logistic.hybrid --glm Logistic/Firth" from_work_dir="plink.glm.logistic.hybrid --glm Logistic/Firth" hidden="True"/> + <data name="OUTPUT_plink_grm __make_grm_list GCTA" format="plink.grm --make-grm-list GCTA" label="${tool.name} on ${on_string}: plink.grm --make-grm-list GCTA" from_work_dir="plink.grm --make-grm-list GCTA" hidden="True"/> + <data name="OUTPUT_plink_grm_N_bin __make_grm_bin GCTA" format="plink.grm.N.bin --make-grm-bin GCTA" label="${tool.name} on ${on_string}: plink.grm.N.bin --make-grm-bin GCTA" from_work_dir="plink.grm.N.bin --make-grm-bin GCTA" hidden="True"/> + <data name="OUTPUT_plink_grm_bin __make_grm_bin GCTA" format="plink.grm.bin --make-grm-bin GCTA" label="${tool.name} on ${on_string}: plink.grm.bin --make-grm-bin GCTA" from_work_dir="plink.grm.bin --make-grm-bin GCTA" hidden="True"/> + <collection name="OUTPUT_plink___gz few BGZipped" type="list" label="plink.*.gz	few	BGZipped" hidden="True"> + <discover_datasets pattern="plink\.(?P<name>)\.gz\	few\	BGZipped" format="plink.*.gz few BGZipped"/> + </collection> + <data name="OUTPUT_plink_haps __export" format="plink.haps --export" label="${tool.name} on ${on_string}: plink.haps --export" from_work_dir="plink.haps --export" hidden="True"/> + <data name="OUTPUT_plink_hardy __hardy Hardy_Weinberg" format="plink.hardy --hardy Hardy-Weinberg" label="${tool.name} on ${on_string}: plink.hardy --hardy Hardy-Weinberg" from_work_dir="plink.hardy --hardy Hardy-Weinberg" hidden="True"/> + <data name="OUTPUT_plink_hardy_x __hardy Graffelman_Weir" format="plink.hardy.x --hardy Graffelman-Weir" label="${tool.name} on ${on_string}: plink.hardy.x --hardy Graffelman-Weir" from_work_dir="plink.hardy.x --hardy Graffelman-Weir" hidden="True"/> + <data name="OUTPUT_plink_het __het Inbreeding" format="plink.het --het Inbreeding" label="${tool.name} on ${on_string}: plink.het --het Inbreeding" from_work_dir="plink.het --het Inbreeding" hidden="True"/> + <collection name="OUTPUT_plink___id lots Ordered" type="list" label="plink.*.id	lots	Ordered" hidden="True"> + <discover_datasets pattern="plink\.(?P<name>)\.id\	lots\	Ordered" format="plink.*.id lots Ordered"/> + </collection> + <data name="OUTPUT_plink_kin0 __make_king_table KING_robust" format="plink.kin0 --make-king-table KING-robust" label="${tool.name} on ${on_string}: plink.kin0 --make-king-table KING-robust" from_work_dir="plink.kin0 --make-king-table KING-robust" hidden="True"/> + <data name="OUTPUT_plink_king __make_king KING_robust" format="plink.king --make-king KING-robust" label="${tool.name} on ${on_string}: plink.king --make-king KING-robust" from_work_dir="plink.king --make-king KING-robust" hidden="True"/> + <data name="OUTPUT_plink_legend __export" format="plink.legend --export" label="${tool.name} on ${on_string}: plink.legend --export" from_work_dir="plink.legend --export" hidden="True"/> + <data name="OUTPUT_plink_normalized __normalize" format="plink.normalized --normalize" label="${tool.name} on ${on_string}: plink.normalized --normalize" from_work_dir="plink.normalized --normalize" hidden="True"/> + <data name="OUTPUT_plink_pgen __make_[b]pgen PLINK" format="plink.pgen --make-[b]pgen PLINK" label="${tool.name} on ${on_string}: plink.pgen --make-[b]pgen PLINK" from_work_dir="plink.pgen --make-[b]pgen PLINK" hidden="True"/> + <data name="OUTPUT_plink_prune_in __indep_pairwise Pruned" format="plink.prune.in --indep-pairwise Pruned" label="${tool.name} on ${on_string}: plink.prune.in --indep-pairwise Pruned" from_work_dir="plink.prune.in --indep-pairwise Pruned" hidden="True"/> + <data name="OUTPUT_plink_prune_out __indep_pairwise IDs" format="plink.prune.out --indep-pairwise IDs" label="${tool.name} on ${on_string}: plink.prune.out --indep-pairwise IDs" from_work_dir="plink.prune.out --indep-pairwise IDs" hidden="True"/> + <data name="OUTPUT_plink_psam __make_pgen___ PLINK" format="plink.psam --make-pgen... PLINK" label="${tool.name} on ${on_string}: plink.psam --make-pgen... PLINK" from_work_dir="plink.psam --make-pgen... PLINK" hidden="True"/> + <data name="OUTPUT_plink_pvar __make_pgen___ PLINK" format="plink.pvar --make-pgen... PLINK" label="${tool.name} on ${on_string}: plink.pvar --make-pgen... PLINK" from_work_dir="plink.pvar --make-pgen... PLINK" hidden="True"/> + <data name="OUTPUT_plink_raw __export" format="plink.raw --export" label="${tool.name} on ${on_string}: plink.raw --export" from_work_dir="plink.raw --export" hidden="True"/> + <data name="OUTPUT_plink_recoverid_dup __recover_var_ids List" format="plink.recoverid.dup --recover-var-ids List" label="${tool.name} on ${on_string}: plink.recoverid.dup --recover-var-ids List" from_work_dir="plink.recoverid.dup --recover-var-ids List" hidden="True"/> + <data name="OUTPUT_plink_rel __make_rel Relationship" format="plink.rel --make-rel Relationship" label="${tool.name} on ${on_string}: plink.rel --make-rel Relationship" from_work_dir="plink.rel --make-rel Relationship" hidden="True"/> + <data name="OUTPUT_plink_rmdup_list __rm_dup" format="plink.rmdup.list --rm-dup" label="${tool.name} on ${on_string}: plink.rmdup.list --rm-dup" from_work_dir="plink.rmdup.list --rm-dup" hidden="True"/> + <data name="OUTPUT_plink_rmdup_mismatch __rm_dup List" format="plink.rmdup.mismatch --rm-dup List" label="${tool.name} on ${on_string}: plink.rmdup.mismatch --rm-dup List" from_work_dir="plink.rmdup.mismatch --rm-dup List" hidden="True"/> + <data name="OUTPUT_plink_sample __export Oxford" format="plink.sample --export Oxford" label="${tool.name} on ${on_string}: plink.sample --export Oxford" from_work_dir="plink.sample --export Oxford" hidden="True"/> + <data name="OUTPUT_plink_scount __sample_counts Sample" format="plink.scount --sample-counts Sample" label="${tool.name} on ${on_string}: plink.scount --sample-counts Sample" from_work_dir="plink.scount --sample-counts Sample" hidden="True"/> + <data name="OUTPUT_plink_sdiff __sample_diff Sample_pair" format="plink.sdiff --sample-diff Sample-pair" label="${tool.name} on ${on_string}: plink.sdiff --sample-diff Sample-pair" from_work_dir="plink.sdiff --sample-diff Sample-pair" hidden="True"/> + <data name="OUTPUT_plink_sdiff_summary __sample_diff Sample_pair" format="plink.sdiff.summary --sample-diff Sample-pair" label="${tool.name} on ${on_string}: plink.sdiff.summary --sample-diff Sample-pair" from_work_dir="plink.sdiff.summary --sample-diff Sample-pair" hidden="True"/> + <data name="OUTPUT_plink_smiss __missing Sample_based" format="plink.smiss --missing Sample-based" label="${tool.name} on ${on_string}: plink.smiss --missing Sample-based" from_work_dir="plink.smiss --missing Sample-based" hidden="True"/> + <data name="OUTPUT_plink_snplist __write_snplist List" format="plink.snplist --write-snplist List" label="${tool.name} on ${on_string}: plink.snplist --write-snplist List" from_work_dir="plink.snplist --write-snplist List" hidden="True"/> + <data name="OUTPUT_plink_sscore __score Sample" format="plink.sscore --score Sample" label="${tool.name} on ${on_string}: plink.sscore --score Sample" from_work_dir="plink.sscore --score Sample" hidden="True"/> + <data name="OUTPUT_plink_traw __export" format="plink.traw --export" label="${tool.name} on ${on_string}: plink.traw --export" from_work_dir="plink.traw --export" hidden="True"/> + <data name="OUTPUT_plink_vcf __export" format="plink.vcf --export" label="${tool.name} on ${on_string}: plink.vcf --export" from_work_dir="plink.vcf --export" hidden="True"/> + <data name="OUTPUT_plink_vmiss __missing Variant_based" format="plink.vmiss --missing Variant-based" label="${tool.name} on ${on_string}: plink.vmiss --missing Variant-based" from_work_dir="plink.vmiss --missing Variant-based" hidden="True"/> + <data name="OUTPUT_plink_vscore __variant_score Text" format="plink.vscore --variant-score Text" label="${tool.name} on ${on_string}: plink.vscore --variant-score Text" from_work_dir="plink.vscore --variant-score Text" hidden="True"/> + <data name="OUTPUT_plink_vscore_bin __variant_score Binary" format="plink.vscore.bin --variant-score Binary" label="${tool.name} on ${on_string}: plink.vscore.bin --variant-score Binary" from_work_dir="plink.vscore.bin --variant-score Binary" hidden="True"/> + <data name="OUTPUT_plink_vscore_cols __variant_score Column" format="plink.vscore.cols --variant-score Column" label="${tool.name} on ${on_string}: plink.vscore.cols --variant-score Column" from_work_dir="plink.vscore.cols --variant-score Column" hidden="True"/> + <data name="OUTPUT_plink_vscore_vars __variant_score Variant" format="plink.vscore.vars --variant-score Variant" label="${tool.name} on ${on_string}: plink.vscore.vars --variant-score Variant" from_work_dir="plink.vscore.vars --variant-score Variant" hidden="True"/> + <collection name="OUTPUT_plink___zst pack Zstd_compressed" type="list" label="plink.*.zst	pack	Zstd-compressed" hidden="True"> + <discover_datasets pattern="plink\.(?P<name>)\.zst\	pack\	Zstd\-compressed" format="plink.*.zst pack Zstd-compressed"/> + </collection> + <data name="OUTPUT_plink_log" format="plink.log" label="${tool.name} on ${on_string}: plink.log" from_work_dir="plink.log" hidden="False"/> + </outputs> + <help><![CDATA[ +:: + + PLINK v2.00a2.3 AVX2 (24 Jan 2020) www.cog-genomics.org/plink/2.0/ + (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 + + In the command line flag definitions that follow, + * <angle brackets> denote a required parameter, where the text between the + angle brackets describes its nature. + * ['square brackets + single-quotes'] denotes an optional modifier. Use the + EXACT text in the quotes. + * [{bar|separated|braced|bracketed|values}] denotes a collection of mutually + exclusive optional modifiers (again, the exact text must be used). When + there are no outer square brackets, one of the choices must be selected. + * ['quoted_text='<description of value>] denotes an optional modifier that + must begin with the quoted text, and be followed by a value with no + whitespace in between. '|' may also be used here to indicate mutually + exclusive options. + * [square brackets without quotes or braces] denote an optional parameter, + where the text between the brackets describes its nature. + * An ellipsis (...) indicates that you may enter multiple parameters of the + specified type. + * A "column set descriptor" is either + 1. a comma-separated sequence of column set names; this is interpreted as + the full list of column sets to include. + 2. a comma-separated sequence of column set names, all preceded by '+' or + '-'; this is interpreted as a list of changes to the default. + + plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...] + plink2 --help [flag name(s)...] + + Most PLINK runs require exactly one main input fileset. The following flags + are available for defining its form and location: + + --pfile <prefix> ['vzs'] : Specify .pgen + .pvar[.zst] + .psam prefix. + --pgen <filename> : Specify full name of .pgen/.bed file. + --pvar <filename> : Specify full name of .pvar/.bim file. + --psam <filename> : Specify full name of .psam/.fam file. + + --bfile <prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix. + --bpfile <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix. + + --keep-autoconv : When importing non-PLINK-binary data, don't delete + autogenerated binary fileset at end of run. + + --no-fid : .fam file does not contain column 1 (family ID). + --no-parents : .fam file does not contain columns 3-4 (parents). + --no-sex : .fam file does not contain column 5 (sex). + + --vcf <filename> ['dosage='<field>] + --bcf <filename> ['dosage='<field>] (not implemented yet) : + Specify full name of .vcf{|.gz|.zst} or BCF2 file to import. + * These can be used with --psam/--fam. + * By default, dosage information is not imported. To import the GP field + (must be VCFv4.3-style 0..1, one probability per possible genotype), add + 'dosage=GP' (or 'dosage=GP-force', see below). To import Minimac3-style + DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else + for now) causes the named field to be interpreted as a Minimac3-style + dosage. + Note that, in the dosage=GP case, PLINK 2 collapses the probabilities + down to dosages; you cannot use PLINK 2 to losslessly convert VCF + FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2 + now errors out when dosage=GP is used on a file with a FORMAT:DS header + line and --import-dosage-certainty wasn't specified, since dosage=DS + extracts the same information more quickly in this situation. You can + suppress this error with 'dosage=GP-force'. + In all of these cases, hardcalls are regenerated from scratch from the + dosages. As a consequence, variants with no GT field can now be + imported; they will be assumed to contain only diploid calls when HDS is + also absent. + + --data <filename prefix> [REF/ALT mode] ['gzs'] + --bgen <filename> [REF/ALT mode] ['snpid-chr'] + --gen <filename> [REF/ALT mode] + --sample <filename> : + Specify an Oxford-format dataset to import. --data specifies a .gen[.zst] + + .sample pair, while --bgen specifies a BGEN v1.1+ file. + * If a BGEN v1.2+ file contains sample IDs, it may be imported without a + companion .sample file. + * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field + instead of the usual chromosome field. + * The following REF/ALT modes are supported: + 'ref-first': The first allele for each variant is REF. + 'ref-last': The last allele for each variant is REF. + 'ref-unknown' (default): The last allele for each variant is treated as + provisional-REF. + This parameter will be required instead of optional in alpha 3. + + --haps <filename> [{ref-first | ref-last}] + --legend <filename> <chr code> : + Specify .haps [+ .legend] file(s) to import. + * When --legend is specified, it's assumed that the --haps file doesn't + contain header columns. + * On chrX, the second male column may contain dummy '-' entries. (However, + PLINK 2 currently cannot handle omitted male columns.) + * If not used with --sample, new sample IDs are of the form 'per#/per#'. + + --map <filename> : Specify full name of .map file. + --import-dosage <allele dosage file> ['noheader'] ['id-delim='<char>] + ['skip0='<i>] ['skip1='<j>] ['skip2='<k>] ['dose1'] + ['format='<m>] [{ref-first | ref-last}] + ['single-chr='<code>] ['chr-col-num='<#>] + ['pos-col-num='<#>] : + Specify PLINK 1.x-style dosage file to import. + * You must also specify a companion .psam/.fam file. + * By default, PLINK assumes that the file contains a header line, which has + 'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column + i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are + normally zero, but can be changed with 'skip0', 'skip1', and 'skip2' + respectively. FID/IID are normally assumed to be separate tokens, but if + they're merged into a single token you can specify the delimiter with + 'id-delim='.) If such a header line is not present, use the 'noheader' + modifier; samples will then be assumed to appear in the same order as + they do in the .psam/.fam file. + * You may specify a companion .map file. If you do not, + * 'single-chr=' can be used to specify that all variants are on the named + chromosome. Otherwise, you can use 'chr-col-num=' to read chromosome + codes from the given (1-based) column number. + * 'pos-col-num=' causes bp coordinates to be read from the given column + number. + * The 'format=' modifier lets you specify the number of values used to + represent each dosage. 'format=1' normally indicates a single 0..2 A1 + expected count; 'dose1' modifies this to a 0..1 frequency. 'format=2' + indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het + likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2. + 'format=infer' (the default) infers the format from the number of columns + in the first nonheader line. + + --dummy <sample ct> <SNP ct> [missing dosage freq] [missing pheno freq] + [{acgt | 1234 | 12}] ['pheno-ct='<count>] ['scalar-pheno'] + ['dosage-freq='<rate>] + This generates a fake input dataset with the specified number of samples + and SNPs. + * By default, the missing dosage and phenotype frequencies are zero. + These can be changed by providing 3rd and 4th numeric parameters. + * By default, allele codes are As and Bs; this can be changed with the + 'acgt', '1234', or '12' modifier. + * By default, one binary phenotype is generated. 'pheno-ct=' can be used + to change the number of phenotypes, and 'scalar-pheno' causes these + phenotypes to be normally distributed scalars. + * By default, all (nonmissing) dosages are in {0,1,2}. To make some of + them take on decimal values, use 'dosage-freq='. (These dosages are + affected by --hard-call-threshold and --dosage-erase-threshold.) + + --fa <filename> : Specify full name of reference FASTA file. + + Output files have names of the form 'plink2.<extension>' by default. You can + change the 'plink2' prefix with + + --out <prefix> : Specify prefix for output files. + + Most runs also require at least one of the following commands: + + --rm-dup [mode] ['list'] + Remove all but one instance of each duplicate-ID variant (ignoring the + missing ID), and (with the 'list' modifier) write a list of duplicated IDs + to <output prefix>.rmdup.list. + The following modes of operation are supported: + * 'error' (default) causes this to error out when there's a genotype data + or other mismatch between the records. A list of affected IDs is written + to <output prefix>.rmdup.mismatch. + * 'retain-mismatch' causes all instances of a duplicate-ID variant to be + retained when there's a genotype data or variant info mismatch; otherwise + one instance is kept. The .rmdup.mismatch file is also written. + * 'exclude-mismatch' removes all instances of duplicate-ID mismatched + variants instead. + * 'exclude-all' causes all instances of duplicate-ID variants to be + removed, even when the actual records are identical. + * 'force-first' causes only the first instance of duplicate-ID variants to + be kept, under all circumstances. + + --make-pgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase'] + ['erase-dosage'] ['pvar-cols='<col set descriptor>] + ['psam-cols='<col set descriptor>] + --make-bpgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase'] + ['erase-dosage'] + --make-bed ['vzs'] ['trim-alts'] + Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] + + .psam, --make-bpgen = .pgen + .bim[.zst] + .fam). + * Unlike the automatic text-to-binary converters (which only heed + chromosome filters), this supports all of PLINK's filtering flags. + * The 'vzs' modifier causes the variant file (.pvar/.bim) to be + Zstd-compressed. + * The 'format' modifier requests an uncompressed fixed-variant-width .pgen + file. (These do not directly support multiallelic variants.) The + following format code is currently supported: + 2: just like .bed, except with an extended (12-byte instead of 3-byte) + header containing variant/sample counts, and rotated genotype codes + (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing). + * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage + information from being written to the new .pgen. + * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT. + Supported optional .pvar column sets are: + xheader: All ## header lines (yeah, this is technically not a column), + except for possibly FILTER/INFO definitions when those + column(s) have been removed. Without this, only the #CHROM + header line is kept. + maybequal: QUAL. Omitted if all remaining values are missing. + qual: Force QUAL column to be written even when empty. + maybefilter: FILTER. Omitted if all remaining values are missing. + filter: Force FILTER column to be written even when empty. + maybeinfo: INFO. Omitted if all remaining values are missing, or if + INFO:PR is the only subfield. + info: Force INFO column to be written. + maybecm: Centimorgan coordinate. Omitted if all remaining values = 0. + cm: Force CM column to be written even when empty. + The default is xheader,maybequal,maybefilter,maybeinfo,maybecm. + * Supported column sets for the .psam file are: + maybefid: Family ID, '0' = missing. Omitted if all values missing. + fid: Force FID column to be written even when empty. + maybesid: Source ID, '0' = missing. Omitted if all values missing. + sid: Force SID column to be written even when empty. + maybeparents: Father and mother IIDs. Omitted if all values missing. + parents: Force PAT and MAT columns to be written even when empty. + sex: '1' = male, '2' = female, 'NA' = missing. + pheno1: First active phenotype. If none, all column entries are set to + the --output-missing-phenotype string. + phenos: All active phenotypes, if any. (Can be combined with pheno1 to + force at least one phenotype column to be written.) + The default is maybefid,maybesid,maybeparents,sex,phenos. + + --make-just-pvar ['zs'] ['cols='<column set descriptor>] + --make-just-psam ['cols='<column set descriptor>] + --make-just-bim ['zs'] + --make-just-fam + Variants of --make-pgen/--make-bed which only write a new variant or sample + file. These don't always require an input genotype file. + USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary + genotype data and your sample/variant indexes if you use these commands + improperly. If you have any doubt, stick with --make-[b]pgen/--make-bed. + + --export <output format(s)...> [{01 | 12}] ['bgz'] ['id-delim='<char>] + ['id-paste='<column set descriptor>] ['include-alt'] + ['omit-nonmale-y'] ['spaces'] ['vcf-dosage='<field>] ['ref-first'] + ['bits='<#>] + Create a new fileset with all filters applied. The following output + formats are supported: + (actually, only A, AD, A-transpose, bgen-1.x, ind-major-bed, haps, + hapslegend, oxford, and vcf are implemented for now) + * '23': 23andMe 4-column format. This can only be used on a single + sample's data (--keep may be handy), and does not support + multicharacter allele codes. + * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R. + If you need uncounted alleles to be named in the header line, add + the 'include-alt' modifier. + * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding. + Also supports 'include-alt'. + * 'A-transpose': Variant-major 0/1/2. + * 'beagle': Unphased per-autosome .dat and .map files, readable by early + BEAGLE versions. + * 'beagle-nomap': Single .beagle.dat file. + * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample + identifiers are stored in the .bgen (with id-delim and + id-paste settings applied), and default precision is 16-bit + (use the 'bits' modifier to reduce this). + * 'bimbam': Regular BIMBAM format. + * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not + support multiple chromosomes. + * 'fastphase': Per-chromosome fastPHASE files, with + .chr-<chr #>.phase.inp filename extensions. + * 'fastphase-1chr': Single .phase.inp file. Does not support + multiple chromosomes. + * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All + data must be biallelic and phased. When the 'bgz' + modifier is present, the .haps file is + block-gzipped. + * 'HV': Per-chromosome Haploview files, with .chr-<chr #>{.ped,.info} + filename extensions. + * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support + multiple chromosomes. + * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam). + * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile. + * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile + + --reference. + * 'list': Single genotype-based list, up to 4 lines per variant. To omit + nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' + modifier. + * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a + genotype-based list which omits the most common genotype for + each variant. Also supports 'omit-nonmale-y'. + * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier is + present, the .gen file is block-gzipped. + * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file. + * 'compound-genotypes': Same as 'ped', except that the space between each + pair of same-variant allele codes is removed. + * 'structure': Structure-format. + * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with + --tfile. + * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are + present, they are automatically merged with chrX, with + proper handling of chromosome codes and male ploidy. + When the 'bgz' modifier is present, the VCF file is + block-gzipped. + The 'id-paste' modifier controls which .psam columns + are used to construct sample IDs (choices are maybefid, + fid, iid, maybesid, and sid; default is + maybefid,iid,maybesid), while the 'id-delim' modifier + sets the character between the ID pieces (default '_'). + Dosages are not exported unless the 'vcf-dosage=' + modifier is present. The following five dosage export + modes are supported: + 'GP': genotype posterior probabilities (v4.3 only). + 'DS': Minimac3-style dosages, omitted for hardcalls. + 'DS-force': Minimac3-style dosages, never omit. + 'HDS': Minimac3-style phased dosages, omitted for + hardcalls and unphased calls. Also includes + 'DS' output. + 'HDS-force': Always report DS and HDS. + In addition, + * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles + to be coded as '2', while '01' maps alt1 -> 0 and ref -> 1. + * The 'spaces' modifier makes the output space-delimited instead of + tab-delimited, whenever both are permitted. + * For biallelic formats where it's unspecified whether the reference/major + allele should appear first or second, --export defaults to second for + compatibility with PLINK 1.9. Use 'ref-first' to change this. + (Note that this doesn't apply to the 'A', 'AD', and 'A-transpose' + formats; use --export-allele to control which alleles are counted there.) + + --freq ['zs'] ['counts'] ['cols='<column set descriptor>] ['bins-only'] + ['refbins='<comma-separated bin boundaries> | 'refbins-file='<file>] + ['alt1bins='<comma-separated bin boundaries> | 'alt1bins-file='<file>] + Empirical allele frequency report. By default, only founders are + considered. Dosages are taken into account (e.g. heterozygous haploid + calls count as 0.5). + Supported column sets are: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + reffreq: Reference allele frequency/dosage. + alt1freq: Alt1 frequency/dosage. + altfreq: Comma-separated frequencies/dosages for all alternate alleles. + freq: Similar to altfreq, except ref is also included at the start. + eq: Comma-separated <allele>=<freq> for all present alleles. (If no + alleles are present, the column contains a single '.'.) + eqz: Same as eq, except zero-counts are included. + alteq/alteqz: Same as eq/eqz, except reference allele is omitted. + numeq: 0=<freq>,1=<freq>, etc. Zero-counts are omitted. + altnumeq: Same as numeq, except reference allele is omitted. + machr2: Unphased MaCH imputation quality metric. + minimac3r2: Phased Minimac3 imputation quality. + nobs: Number of allele observations. + The default is chrom,ref,alt,altfreq,nobs. + Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with + 'counts') file(s) are generated when 'refbins='/'refbins-file=' or + 'alt1bins='/'alt1bins-file=' is present; these report the total number of + frequencies or counts in each left-closed, right-open interval. (If you + only want these histogram(s), and not the main report, add 'bins-only'.) + + --geno-counts ['zs'] ['cols='<column set descriptor>] + Variant-based hardcall genotype count report (considering both alleles + simultaneously in the diploid case). Nonfounders are now included; use + --keep-founders if this is a problem. Heterozygous haploid calls are + treated as missing. + Supported column sets are: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + homref: Homozygous-ref count. + refalt1: Heterozygous ref-alt1 count. + refalt: Comma-separated het ref-altx counts. + homalt1: Homozygous-alt1 count. + altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-... + order. + xy: Similar to altxy, except the reference allele is treated as alt0, + and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-... + hapref: Haploid-ref count. + hapalt1: Haploid-alt1 count. + hapalt: Comma-separated haploid-altx counts. + hap: Similar to hapalts, except ref is also included at the start. + numeq: 0/0=<hom ref ct>,0/1=<het ref-alt1>,1/1=<hom alt1>,...,0=<hap ref> + etc. Zero-counts are omitted. (If all genotypes are missing, the + column contains a single '.'.) + missing: Number of missing genotypes. + nobs: Number of (nonmissing) genotype observations. + The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing. + + --sample-counts ['zs'] ['cols='<column set descriptor>] + Sample-based hardcall genotype count report. + * Unknown-sex samples are treated as female. + * Heterozygous haploid calls (MT included) are treated as missing. + * As with other PLINK 2 commands, SNPs that have not been left-normalized + are counted as non-SNP non-symbolic. (Use e.g. --normalize when that's a + problem.) + * Supported column sets are: + maybefid: FID, if that column was present in the input. + fid: Force FID column to be written even when absent in the input. + (IID is always present, and positioned here.) + maybesid: SID, if that column was present in the input. + sid: Force SID column to be written even when absent in the input. + sex: '1' = male, '2' = female, 'NA' = missing. + hom: Homozygous genotype count. + homref: Homozygous-ref genotype count. + homalt: Homozygous-alt genotype count. + homaltsnp: Homozygous-alt SNP count. + het: Heterozygous genotype count. + refalt: Heterozygous ref-altx genotype count. + het2alt: Heterozygous altx-alty genotype count. + hetsnp: Heterozygous SNP count. + dipts: Diploid SNP transition count. + ts: SNP transition count (excluding chrY for females). + diptv: Diploid SNP transversion count. + tv: SNP transversion count. + dipnonsnpsymb: Diploid non-SNP, non-symbolic count. + nonsnpsymb: Non-SNP, non-symbolic count. + symbolic: Symbolic variant count. + nonsnp: Non-SNP count. + dipsingle: Number of singletons relative to this dataset, across just + diploid calls. (Note that if the ALT allele in a chrX + biallelic variant appears in exactly one female and one + male, that counts as a singleton for just the female.) + single: Number of singletons relative to this dataset. + haprefwfemaley: Haploid-ref count, counting chrY for everyone. + hapref: Haploid-ref count, excluding chrY for females. + hapaltwfemaley: Haploid-alt count, counting chrY for everyone. + hapalt: Haploid-alt count, excluding chrY for females. + missingwfemaley: Missing call count, counting chrY for everyone. + missing: Missing call count, excluding chrY for females. + The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv, + dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley. + * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb', + 'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous + altx-alty call separately, since they can be of different subtypes. + (I.e. if they are of the same subtype, the corresponding count is + incremented by 2.) As a consequence, these columns are unaffected by + variant split/join. + + --missing ['zs'] [{sample-only | variant-only}] + ['scols='<column set descriptor>] ['vcols='<column set descriptor>] + Generate sample- and variant-based missing data reports (or just one report + if 'sample-only'/'variant-only' is specified). + As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats. + Supported column sets in the sample-based report are: + maybefid: FID, if that column was present in the input. + fid: Force FID column to be written even when absent in the input. + (IID is always present, and positioned here.) + maybesid: SID, if that column was present in the input. + sid: Force SID column to be written even when absent in the input. + misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no + phenotypes are loaded. + missphenos: A Y/N column for each loaded phenotype. (Can be combined + with misspheno1 to force at least one such column.) + nmissdosage: Number of missing dosages. + nmiss: Number of missing hardcalls, not counting het haploids. + nmisshh: Number of missing hardcalls, counting het haploids. + hethap: Number of heterozygous haploid hardcalls. + nobs: Denominator (male count on chrY, otherwise total sample count). + fmissdosage: Missing dosage rate. + fmiss: Missing hardcall rate, not counting het haploids. + fmisshh: Missing hardcall rate, counting het haploids. + The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss. + Supported column sets in the variant-based report are: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + nmissdosage: Number of missing dosages. + nmiss: Number of missing hardcalls, not counting het haploids. + nmisshh: Number of missing hardcalls, counting het haploids. + hethap: Number of heterozygous haploid calls. + nobs: Number of potentially valid calls. + fmissdosage: Missing dosage rate. + fmiss: Missing hardcall rate, not counting het haploids. + fmisshh: Missing hardcall rate, counting het haploids. + fhethap: Heterozygous haploid rate. + The default is chrom,nmiss,nobs,fmiss. + + --hardy ['zs'] ['midp'] ['redundant'] ['cols='<column set descriptor>] + Hardy-Weinberg exact test p-value report(s). + * By default, only founders are considered; change this with --nonfounders. + * chrX is now omitted from the main <output prefix>.hardy report. Instead, + (if present) it gets its own <output prefix>.hardy.x report based on the + method described in Graffelman J, Weir BS (2016) Hardy-Weinberg + equilibrium and the X chromosome. + * For variants with k alleles where k>2, k separate 'biallelic' tests are + performed, each reported on its own line. However, biallelic variants + are normally reported on a single line, since the counts/frequencies + would be mirror-images and the p-values would be the same. You can add + the 'redundant' modifier to force biallelic variant results to be + reported on two lines for parsing convenience. + * There is currently no special handling of case/control phenotypes. + Supported column sets are: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + (A1 is always present, and positioned here.) + ax: Non-A1 allele(s), comma-separated. + gcounts: Hom-A1 count, total number of het-A1 calls, and total number of + nonmissing calls with no copies of A1. On chrX, these are + followed by male A1 and male non-A1 counts. + gcount1col: gcounts values in a single comma-separated column. + hetfreq: Observed and expected het-A1 frequencies. + sexaf: Female and male A1 observed allele frequencies (chrX only). + femalep: Female-only p/midp-value (chrX only). + p: Hardy-Weinberg equilibrium exact test p/midp-value. + The default is chrom,ax,gcounts,hetfreq,sexaf,p. + + --indep-pairwise <window size>['kb'] [step size (variant ct)] + <unphased-hardcall-r^2 threshold> + Generate a list of variants in approximate linkage equilibrium. + * For multiallelic variants, major allele counts are used in the r^2 + computation. + * With the 'kb' modifier, the window size is in kilobase instead of variant + count units. (Pre-'kb' space is optional, i.e. + "--indep-pairwise 500 kb 0.5" and "--indep-pairwise 500kb 0.5" have the + same effect.) + * The step size now defaults to 1 if it's unspecified, and *must* be 1 if + the window is in kilobase units. + * Note that you need to rerun PLINK using --extract or --exclude on the + .prune.in/.prune.out file to apply the list to another computation... and + as with other applications of --extract/--exclude, duplicate variant IDs + are a problem. --indep-pairwise still runs to completion for now when + duplicate variant IDs are present, but that will become an error in alpha + 3. + + --ld <variant ID> <variant ID> ['dosage'] ['hwe-midp'] + This displays diplotype frequencies, r^2, and D' for a single pair of + variants. + * For multiallelic variants, major allele counts/dosages are used. + * Phase information is used when both variants are on the same chromosome. + * When there is at least one sample with unphased het calls for both + variants, diplotype frequencies are estimated using the Hill equation. + If there are multiple biologically possible local maxima, all are + displayed, along with HWE exact test statistics. + * By default, only hardcalls are considered. Add the 'dosage' modifier if + you want dosages to be taken into account. (In the diploid case, an + unphased dosage of x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x + is in 0..1.) + + --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>] + ['include-missing'] [{pairwise | counts-only}] + ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>] + ['counts-cols='<column set descriptor>] + {base= | ids=}<sample ID> [other sample ID(s)...] + --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>] + ['include-missing'] [{pairwise | counts-only}] + ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>] + ['counts-cols='<column set descriptor>] file=<ID-pair file> + (alias: --sdiff) + Report discordances and discordance-counts between pairs of samples. If + chrX or chrY is present, sex must be defined and consistent. + * There are three ways to specify which sample pairs to compare. To + compare a single baseline sample against some others, start the + (space-delimited) sample ID list with 'base='. To perform an all-vs.-all + comparison, start it with 'ids=' instead. To compare sample pairs listed + in a file, use 'file='. + Note that 'base='/'ids='/'file=' must be positioned after all modifiers. + * Sample IDs are interpreted as if they were in a VCF header line, with + 'id-delim=' having the usual effect. + * By default, comparisons are based on hardcalls. Use 'dosage' to compare + dosages instead; you can combine this with a tolerance in [0, 0.5). + * By default, if one genotype is missing and the other isn't, that doesn't + count as a difference; this can be changed with 'include-missing'. + * By default, a single main report is written to + <output prefix>[.<base ID>].sdiff. To write separate pairwise + <output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add + the 'pairwise' modifier. To omit the main report, add the 'counts-only' + modifier. (Note that, if you're only interested in nonmissing autosomal + biallelic hardcalls, --make-king-table provides a more efficient way to + compute just counts.) + * By default, if an output filename has a multipart sample ID, the parts + will be delimited by '_'; use 'fname-id-delim=' to change this. + Supported main-report column sets are: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (Variant ID is always present, and positioned here.) + ref: Reference allele. + alt: All alternate alleles, comma-separated. + maybefid: FID1/FID2, if that column was in the input. Requires 'id'. + fid: Force FID1/FID2 even when FID was absent in the input. + id: IID1/IID2. + maybesid: SID1/SID2, if that column was in the input. Requires 'id'. + sid: Force SID1/SID2 even when SID was absent in the input. + geno: Unphased GT or DS for the two samples. + The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the + sample IDs are removed from the default in 'pairwise' mode. + Supported discordance-count-summary column sets are: + maybefid: FID1/FID2, if that column was in the input. + fid: Force FID1/FID2 even when FID was absent in the input. + (IID1/IID2 are always present.) + maybesid: SID1/SID2, if that column was in the input. + sid: Force SID1/SID2 even when SID was absent in the input. + nobs: Number of variants considered. This includes variants where one or + both variants are missing iff 'include-missing' was specified. + nobsibs: ibs0+ibs1+ibs2. + ibs0: Number of diploid variants with no common hardcall alleles. + ibs1: Number of diploid variants with exactly 1 common hardcall allele. + ibs2: Number of diploid variants with both hardcall alleles matching. + halfmiss: Number of variants with exactly 1 missing genotype/dosage. + Ignored without 'include-missing'. + diff: Total number of differences. + The default is maybefid,maybesid,nobs,halfmiss,diff. + + --make-king [{square | square0 | triangle}] [{zs | bin | bin4}] + KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC, + Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in + genome-wide association studies. By default, this writes a + lower-triangular tab-delimited table of kinship coefficients to + <output prefix>.king, and a list of the corresponding sample IDs to + <output prefix>.king.id. The first row of the .king file contains a single + <genome 1-genome 2> kinship coefficient, the second row has the + <genome 1-genome 3> and <genome 2-genome 3> kinship values in that order, + etc. + * Only autosomes are currently considered. + * Pedigree information is currently ignored; the between-family estimator + is used for all pairs. + * For multiallelic variants, REF allele counts are used. + * If the 'square' or 'square0' modifier is present, a square matrix is + written instead; 'square0' fills the upper right triangle with zeroes. + * If the 'zs' modifier is present, the .king file is Zstd-compressed. + * If the 'bin' modifier is present, a binary (square) matrix of + double-precision floating point values, suitable for loading from R, is + instead written to <output prefix>.king.bin. ('bin4' specifies + single-precision numbers instead.) This can be combined with 'square0' + if you still want the upper right zeroed out, or 'triangle' if you don't + want to pad the upper right at all. + * The computation can be subdivided with --parallel. + --make-king-table ['zs'] ['counts'] ['rel-check'] ['cols='<col set descrip.>] + Similar to --make-king, except results are reported in KING's original + .kin0 text table format (with minor changes, e.g. row order is more + friendly to incremental addition of samples), --king-table-filter can be + used to restrict the report to high kinship values, and the 'rel-check' + modifier can be used to restrict to same-FID pairs. + Supported column sets are: + maybefid: FID1/FID2, if that column was in the input. Requires 'id'. + fid: Force FID1/FID2 even when FID was absent in the input. + id: IID1/IID2 (column headers are actually 'ID1'/'ID2' to match KING). + maybesid: SID1/SID2, if that column was in the input. Requires 'id'. + sid: Force SID1/SID2 even when SID was absent in the input. + nsnp: Number of variants considered (autosomal, neither call missing). + hethet: Proportion/count of considered call pairs which are het-het. + ibs0: Proportion/count of considered call pairs which are opposite homs. + ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts. + kinship: KING-robust between-family kinship estimator. + The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship. + hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is + present. If id is omitted, a .kin0.id file is also written. + + --make-rel ['cov'] ['meanimpute'] [{square | square0 | triangle}] + [{zs | bin | bin4}] + Write a lower-triangular variance-standardized relationship matrix to + <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id. + * This computation assumes that variants do not have very low MAF, or + deviate greatly from Hardy-Weinberg equilibrium. + * Also, it's usually best to perform this calculation on a variant set in + approximate linkage equilibrium. + * The 'cov' modifier replaces the variance-standardization step with basic + mean-centering, causing a covariance matrix to be calculated instead. + * The computation can be subdivided with --parallel. + --make-grm-list ['cov'] ['meanimpute'] ['zs'] [{id-header | iid-only}] + --make-grm-bin ['cov'] ['meanimpute'] [{id-header | iid-only}] + --make-grm-list causes the relationships to be written to GCTA's original + list format, which describes one pair per line, while --make-grm-bin writes + them in GCTA 1.1+'s single-precision triangular binary format. Note that + these formats explicitly report the number of valid observations (where + neither sample has a missing call) for each pair, which is useful input for + some scripts. + + --pca [count] [{approx | meanimpute}] ['scols='<col set descriptor>] + --pca [{biallelic-var-wts | var-wts}] [count] [{approx | meanimpute}] ['vzs'] + ['scols='<col set descriptor>] ['vcols='<col set descriptor>] + Extracts top principal components from the variance-standardized + relationship matrix. + * It is usually best to perform this calculation on a variant set in + approximate linkage equilibrium, with no very-low-MAF variants. + * By default, 10 PCs are extracted; you can adjust this by passing a + numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of + 20; this is due to the randomized algorithm's memory footprint growing + quadratically w.r.t. the PC count.) + * The 'approx' modifier causes the standard deterministic computation to be + replaced with the randomized algorithm originally implemented for + Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, + Price AL (2016) Fast Principal-Component Analysis Reveals Convergent + Evolution of ADH1B in Europe and East Asia. This can be a good idea when + you have >5k samples. + * The randomized algorithm always uses mean imputation for missing genotype + calls. For comparison purposes, you can use the 'meanimpute' modifier to + request this behavior for the standard computation. + * 'scols=' can be used to customize how sample IDs appear in the .eigenvec + file. (maybefid, fid, maybesid, and sid supported; default is + maybefid,maybesid.) + * The 'biallelic-var-wts' modifier requests an additional + one-line-per-variant .eigenvec.var file with PCs expressed as variant + weights instead of sample weights, with the condition that all variants + must be biallelic. When it's present, 'vzs' causes the .eigenvec.var + file to be Zstd-compressed. + 'vcols=' can be used to customize the report columns; supported column + sets are: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + maj: Major allele. + nonmaj: All nonmajor alleles, comma-separated. + (PCs are always present, and positioned here. Signs are w.r.t. the + major, not necessarily reference, allele.) + Default is chrom,maj,nonmaj. + * In this build, 'var-wts' generates the same report as biallelic-var-wts, + except with the "all variants must be biallelic" restriction lifted. + This is temporary. It will no longer be supported as of alpha 3; + instead, there will be an 'allele-wts' mode which seamlessly handles + multiallelic variants, at the cost of generating more verbose + one-line-per-allele output. + + --king-cutoff [.king.bin + .king.id fileset prefix] <threshold> + Exclude one member of each pair of samples with KING-robust kinship greater + than the given threshold. Remaining/excluded sample IDs are written to + <output prefix>.king.cutoff.in.id + .king.cutoff.out.id. + If present, the .king.bin file must be triangular (either precision is ok). + + --write-covar ['cols='<column set descriptor>] + If covariates are defined, an updated version (with all filters applied) is + automatically written to <output prefix>.cov whenever --make-pgen, + --make-just-psam, --export, or a similar command is present. However, if + you do not wish to simultaneously generate a new sample file, you can use + --write-covar to just produce a pruned covariate file. + Supported column sets are: + maybefid: FID, if that column was in the input. + fid: Force FID column to be written even when absent in the input. + maybesid: SID, if that column was in the input. + sid: Force SID column to be written even when absent in the input. + maybeparents: Father/mother IIDs ('0' = missing), if columns in input. + parents: Force PAT/MAT columns to be written even when absent in input. + sex: '1' = male, '2' = female, 'NA' = missing. + pheno1: First active phenotype. If none, all column entries are set to + the --output-missing-phenotype string. + phenos: All active phenotypes, if any. (Can be combined with pheno1 to + force at least one phenotype column to be written.) + (Covariates are always present, and positioned here.) + The default is maybefid,maybesid. + + --write-samples + Report IDs of all samples which pass your filters/inclusion thresholds. + + --write-snplist ['zs'] + List all variants which pass your filters/inclusion thresholds. + + --glm ['zs'] ['omit-ref'] [{sex | no-x-sex}] ['log10'] ['pheno-ids'] + [{genotypic | hethom | dominant | recessive}] ['interaction'] + ['hide-covar'] ['intercept'] [{no-firth | firth-fallback | firth}] + ['cols='<col set desc.>] ['local-covar='<file>] ['local-pvar='<file>] + ['local-psam='<file>] ['local-omit-last' | 'local-cats='<category ct>] + Basic association analysis on quantitative and/or case/control phenotypes. + For each variant, a linear (for quantitative traits) or logistic (for + case/control) regression is run with the phenotype as the dependent + variable, and nonmajor allele dosage(s) and a constant-1 column as + predictors. + * There is usually an additive effect line for every nonmajor allele, and + no such line for the major allele. To omit REF alleles instead of major + alleles, add the 'omit-ref' modifier. (When performing interaction + testing, this tends to cause the multicollinearity check to fail for + low-ref-frequency variants.) + * By default, sex (male = 1, female = 2; note that this is a change from + PLINK 1.x) is automatically added as a predictor for X chromosome + variants, and no others. The 'sex' modifier causes it to be added + everywhere (except chrY), while 'no-x-sex' excludes it entirely. + * The 'log10' modifier causes p-values to be reported in -log10(p) form. + * 'pheno-ids' causes the samples used in each set of regressions to be + written to an .id file. (When the samples differ on chrX or chrY, .x.id + and/or .y.id files are also written.) + * The 'genotypic' modifier adds an additive effect/dominance deviation 2df + joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and + 0..1..0 coding instead. + * 'dominant' and 'recessive' specify a model assuming full dominance or + recessiveness, respectively, for the ref allele. I.e. the genotype + column is recoded as 0..1..1 or 0..0..1, respectively. + * 'interaction' adds genotype x covariate interactions to the model. Note + that this tends to produce 'NA' results (due to the multicollinearity + check) when the reference allele is 'wrong'; --maj-ref can be used to + enable analysis of those variants. + * Additional predictors can be added with --covar. By default, association + statistics are reported for all nonconstant predictors; 'hide-covar' + suppresses covariate-only results, while 'intercept' causes intercepts + to be reported. + * For logistic regression, when the phenotype [quasi-]separates the + genotype, an NA result is currently reported by default. To fall back on + Firth logistic regression instead when the basic logistic regression + fails to converge, add the 'firth-fallback' modifier (highly recommended, + will become the default when beta testing begins). To eliminate the + special case and use Firth logistic regression everywhere, add 'firth'. + 'no-firth' can be used to prevent Firth regression from being attempted + in a way that'll still work after alpha testing completes. + * To add covariates which are not constant across all variants, add the + 'local-covar=', 'local-pvar=', and 'local-psam=' modifiers, and use full + filenames for each. + Normally, the local-covar file should have c * n real-valued columns, + where the first c columns correspond to the first sample in the + local-psam file, columns (c+1) to 2c correspond to the second sample, + etc.; and the mth line corresponds to the mth nonheader line of the + local-pvar file. (Variants outside of the local-pvar file are excluded + from the regression.) The local covariates are assigned the names + LOCAL1, LOCAL2, etc.; to exclude the last local covariate from the + regression (necessary if they are e.g. local ancestry coefficients which + sum to 1), add 'local-omit-last'. + Alternatively, with 'local-cats='<k>, the local-covar file is expected to + have n columns with integer-valued entries in [1, k]. These category + assignments are expanded into (k-1) local covariates in the usual manner. + The main report supports the following column sets: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + (A1 is always present, and positioned here. For multiallelic variants, + this column may contain multiple comma-separated alleles when the result + doesn't depend on which allele is A1.) + ax: Non-A1 alleles, comma-separated. + a1count: A1 allele count (can be decimal with dosage data). + totallele: Allele observation count (can be higher than --freq value, due + to inclusion of het haploids and chrX model). + a1countcc: A1 count in cases, then controls (case/control only). + totallelecc: Case and control allele observation counts. + gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases, + then controls (case/control only). + a1freq: A1 allele frequency. + a1freqcc: A1 frequency in cases, then controls (case/control only). + machr2: Unphased MaCH imputation quality (frequently labeled 'INFO'). + firth: Reports whether Firth regression was used (firth-fallback only). + test: Test identifier. (Required unless only one test is run.) + nobs: Number of samples in the regression. + beta: Regression coefficient (for A1 if additive test). + orbeta: Odds ratio for case/control, beta for quantitative traits. + (Ignored if 'beta' column set included.) + se: Standard error of beta. + ci: Bounds of symmetric approximate confidence interval (requires --ci). + tz: T-statistic for linear regression, Wald Z-score for logistic/Firth. + p: Asymptotic p-value (or -log10(p)) for T/Z-statistic. + err: Error code for NA results. + The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p. + + --score <filename> [i] [j] [k] [{header | header-read}] + [{center | variance-standardize | dominant | recessive}] + ['no-mean-imputation'] ['se'] ['zs'] ['ignore-dup-ids'] + [{list-variants | list-variants-zs}] ['cols='<col set descriptor>] + Apply linear scoring system(s) to each sample. + The input file should have one line per scored variant. Variant IDs are + read from column #i and allele codes are read from column #j, where i + defaults to 1 and j defaults to i+1. For now, only one allele per + multiallelic variant may be assigned an explicit score; contact us if you + need this changed. + * By default, a single column of input coefficients is read from column #k, + where k defaults to j+1. (--score-col-nums can be used to specify + multiple columns.) + * 'header-read' causes the first line of the input file to be treated as a + header line containing score names. Otherwise, score(s) are assigned the + names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line + to be entirely ignored. + * By default, copies of unnamed alleles contribute zero to score, while + missing genotypes contribute an amount proportional to the loaded (via + --read-freq) or imputed allele frequency. To throw out missing + observations instead (decreasing the denominator in the final average + when this happens), use the 'no-mean-imputation' modifier. + * You can use the 'center' modifier to shift all genotypes to mean zero, or + 'variance-standardize' to linearly transform the genotypes to mean-0, + variance-1. + * The 'dominant' modifier causes dosages greater than 1 to be treated as 1, + while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes. + ('dominant', 'recessive', and 'variance-standardize' cannot be used with + chrX.) + * The 'se' modifier causes the input coefficients to be treated as + independent standard errors; in this case, standard errors for the score + average/sum are reported. (Note that this will systematically + underestimate standard errors when scored variants are in LD.) + * By default, --score errors out if a variant ID in the input file appears + multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to + skip them instead (a warning is still printed if such variants are + present). + * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to + be written to <output prefix>.sscore.vars[.zst]. + The main report supports the following column sets: + maybefid: FID, if that column was in the input. + fid: Force FID column to be written even when absent in the input. + (IID is always present, and positioned here.) + maybesid: SID, if that column was in the input. + sid: Force SID column to be written even when absent in the input. + pheno1: First active phenotype. + phenos: All active phenotypes, if any. + nmissallele: Number of nonmissing alleles. + denom: Denominator of score average (equal to nmissallele value when + 'no-mean-imputation' specified). + dosagesum: Sum of named allele dosages. + scoreavgs: Score averages. + scoresums: Score sums. + The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs. + For more sophisticated polygenic risk scoring, we recommend the PRSice-2 + software package (https://www.prsice.info/ ). + + --variant-score <filename> ['zs'] ['bin' | 'cols='<col set descriptor>] + (alias: --vscore) + Apply linear scoring system(s) to each variant. Each reported variant + score is the dot product of a sample-weight vector with the + total-ALT-dosage vector, with MAF-based mean imputation applied to missing + dosages. + Input file format: one line per sample, each starting with an ID and + followed by scoring weight(s); it can also have a header line with the + sample ID representation and the score name(s). + The usual .vscore text report supports the following column sets: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + altfreq: ALT allele frequency used for mean-imputation. + nmiss: Number of missing (and thus mean-imputed) dosages. + nobs: Number of (nonmissing) sample observations. + (Variant scores are always present, and positioned here.) + Default is chrom,pos,ref,alt. + If binary output is requested instead, the main .vscore.bin matrix contains + double-precision floating-point values, column (score) ID(s) are saved to a + <output prefix>.vscore.cols, and variant IDs are saved to + <output prefix>.vscore.vars[.zst]. + + --adjust-file <filename> ['zs'] ['gc'] ['cols='<column set descriptor>] + ['log10'] ['input-log10'] ['test='<test name, case-sensitive>] + Given a file with unfiltered association test results, report some basic + multiple-testing corrections, sorted in increasing-p-value order. + * 'gc' causes genomic-controlled p-values to be used in the formulas. + (This tends to be overly conservative. We note that LD Score regression + usually does a better job of calibrating lambda; see Lee JJ, McGue M, + Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an + estimator of confounding and genetic correlations in genome-wide + association studies.) + * 'log10' causes negative base 10 logs of p-values to be reported, instead + of raw p-values. 'input-log10' specifies that the input file contains + -log10(p) values. + * If the input file contains multiple tests per variant which are + distinguished by a 'TEST' column (true for --linear/--logistic/--glm), + you must use 'test=' to select the test to process. + The following column sets are supported: + chrom: Chromosome ID. + pos: Base-pair coordinate. + (ID is always present, and positioned here.) + ref: Reference allele. + alt1: Alternate allele 1. + alt: All alternate alleles, comma-separated. + a1: Tested allele. (Omitted if missing from input file.) + unadj: Unadjusted p-value. + gc: Devlin & Roeder (1999) genomic control corrected p-value (additive + models only). + qq: P-value quantile. + bonf: Bonferroni correction. + holm: Holm-Bonferroni (1979) adjusted p-value. + sidakss: Sidak single-step adjusted p-value. + sidaksd: Sidak step-down adjusted p-value. + fdrbh: Benjamini & Hochberg (1995) step-up false discovery control. + fdrby: Benjamini & Yekutieli (2001) step-up false discovery control. + Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby. + --genotyping-rate ['dosage'] + Report genotyping rate in log (this was automatic in PLINK 1.x). + + --pgen-info + Reports basic information about a .pgen file. + + --validate + Validates all variant records in a .pgen file. + + --zst-decompress <.zst file> [output filename] + (alias: --zd) + Decompress a Zstd-compressed file. If no output filename is specified, the + file is decompressed to standard output. + This cannot be used with any other flags, and does not cause a log file to + be generated. + + The following other flags are supported. + --script <fname> : Include command-line options from file. + --rerun [log] : Rerun commands in log (default 'plink2.log'). + --version : Display only version number before exiting. + --silent : Suppress regular output to console. (Error-output is + not suppressed.) + --double-id : Set both FIDs and IIDs to the VCF/.bgen sample ID. + --const-fid [ID] : Set all FIDs to the given constant. If '0' (the + default), no FID column is created. + --id-delim [d] : Normally parses single-delimiter sample IDs as + <FID><d><IID>, and double-delimiter IDs as + <FID><d><IID><d><SID>; default delimiter is '_'. + --id-delim can no longer be used with + --double-id/--const-fid; it will error out if any ID + lacks the delimiter. + --idspace-to <c> : Convert spaces in VCF/.bgen sample IDs to the given + character. + --iid-sid : Make --id-delim and --sample-diff interpret two-token + sample IDs as IID-SID instead of FID-IID. + --vcf-require-gt : Skip variants with no GT field. + --vcf-min-gq <val> : No-call genotypes when GQ is present and below the + threshold. + --vcf-max-dp <val> : No-call genotypes when DP is present and above/below + --vcf-min-dp <val> the threshold. + --vcf-half-call <m> : Specify how '0/.' and similar VCF GT values should be + handled. The following four modes are supported: + * 'error'/'e' (default) errors out and reports line #. + * 'haploid'/'h' treats them as haploid calls. + * 'missing'/'m' treats them as missing. + * 'reference'/'r' treats the missing value as 0. + --oxford-single-chr <chr name> : Specify single-chromosome .gen/.bgen file + with no useful chromosome info inside. + --missing-code [string list] : Comma-delimited list of missing phenotype + (alias: --missing_code) values for Oxford-format import (default + 'NA'). + --hard-call-threshold <val> : When importing dosage data, a hardcall is + normally saved when the distance from the + nearest hardcall, defined as + 0.5 * sum_i |x_i - round(x_i)| + (where the x_i's are 0..2 allele dosages), + is not greater than 0.1. You can adjust + this threshold by providing a numeric + parameter to --hard-call-threshold. + You can also use this with --make-[b]pgen + to alter the saved hardcalls while leaving + the dosages untouched, or --make-bed to + tweak hardcall export. + --dosage-erase-threshold <val> : --hard-call-threshold normally preserves + the original dosages, and several PLINK 2 + commands use them when they're available. + Use --dosage-erase-threshold to make PLINK + 2 erase dosages and keep only hardcalls + when distance-from-hardcall <= the given + level. + --import-dosage-certainty <val> : The PLINK 2 file format currently supports + a single dosage for each allele. Some + other dosage file formats include a + separate probability for every possible + genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52, + P(1/1)=0.28}, a highly uncertain call that + is nevertheless treated as a hardcall under + '--hard-call-threshold 0.1'. To make PLINK + 2 treat a dosage as missing whenever the + largest probability is less than a + threshold, use --import-dosage-certainty. + --input-missing-genotype <c> : '.' is always interpreted as a missing + genotype code in input files. By default, '0' + also is; you can change this second missing + code with --input-missing-genotype. + --allow-extra-chr : Permit unrecognized chromosome codes (alias --aec). + --chr-set <autosome ct> ['no-x'] ['no-y'] ['no-xy'] ['no-mt'] : + Specify a nonhuman chromosome set. The first parameter sets the number of + diploid autosome pairs if positive, or haploid chromosomes if negative. + Given diploid autosomes, the remaining modifiers indicate the absence of + the named non-autosomal chromosomes. + --cow/--dog/--horse/--mouse/--rice/--sheep : Shortcuts for those species. + --autosome-num <val> : Alias for '--chr-set <value> no-y no-xy no-mt'. + --human : Explicitly specify human chromosome set, and make + output .pvar/VCF files include a ##chrSet header + line. (.pvar/VCF output files automatically + include ##chrSet when a nonhuman set is specified.) + --chr-override ['file'] : By default, if --chr-set/--autosome-num/--cow/etc. + conflicts with an input file ##chrSet header line, + PLINK 2 will error out. --chr-override with no + parameter causes the command line to take + precedence; '--chr-override file' defers to the + file. + --var-min-qual <val> : Skip variants with low/missing QUAL. + --var-filter [exception(s)...] : Skip variants which have FILTER failures. + --extract-if-info <key> <op> <val> : Exclude variants which don't/do satisfy + --exclude-if-info <key> <op> <val> a comparison predicate on an INFO key, + (aliases: --extract-if, e.g. + --exclude-if) --extract-if-info "VT == SNP" + Unless the operator is !=, the predicate + always evaluates to false when the key + is missing. + --require-info <key(s)...> : Exclude variants based on nonexistence + --require-no-info <key(s)...> or existence of an INFO key. "<key>=." + is treated as nonexistence. + --extract-col-cond <f> [valcol] [IDcol] [skip] : + --extract-col-cond-match <(sub)string(s)...> + --extract-col-cond-mismatch <(sub)string(s)...> + --extract-col-cond-substr + --extract-col-cond-min <min> + --extract-col-cond-max <max> : + Exclude all variants without a value-column entry satisfying a condition. + * By default, values are read from column 2 of the file, and variant IDs + are read from column 1. + * Three types of conditions are supported: + * When --extract-col-cond-match is specified without + --extract-col-cond-substr, the value is checked for equality with the + given strings, and kept iff one of them matches. Similarly, + --extract-col-cond-mismatch without --extract-col-cond-substr causes + the variant to be kept iff the value matches none of the given strings. + * When --extract-col-cond-match and/or -mismatch are specified with + --extract-col-cond-substr, the variant is kept iff none of the + --extract-col-cond-mismatch substrings are contained in the value, and + either --extract-col-cond-match was unspecified or at least one of its + substrings is contained. + * Otherwise, the value is interpreted as a number, and the variant is + kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX). + --pheno ['iid-only'] <f> : Specify additional phenotype/covariate file. + Comma-delimited files with a header line are now + permitted. + --pheno-name <name...> : Only load the designated phenotype(s) from the + --pheno (if one was specified) or .psam (if no + --pheno) file. Separate multiple names with + spaces or commas, and use dashes to designate + ranges. + --pheno-col-nums <#...> : Only load the phenotype(s) in the designated + column number(s) from the --pheno file. + --no-psam-pheno : Ignore phenotype(s) in .psam/.fam file. + --strict-sid0 : By default, if there is no SID column in the .psam/.fam + (or --update-ids) file, but there is one in another + input file (for e.g. --keep/--remove), the latter SID + column is ignored; sample IDs are considered matching as + long as FID and IID are equal (with missing FID treated + as '0'). If you also want to require SID = '0' for a + sample ID match in this situation, add --strict-sid0. + --input-missing-phenotype <v> : Set nonzero number to treat as a missing + pheno/covar in input files (default -9). + --no-input-missing-phenotype : Don't treat any nonzero number as a missing + pheno/covar. ('NA'/'nan' are still treated + as missing.) + --1 : Expect case/control phenotypes in input files + to be coded as 0 = control, 1 = case, instead + of the usual 0 = missing, 1 = ctrl, 2 = case. + (Unlike PLINK 1.x, this does not force all + phenotypes to be interpreted as case/ctrl.) + --missing-catname <str> : Set missing-categorical-phenotype string + (case-sensitive, default 'NONE'). + --covar ['iid-only'] <f> : Specify additional covariate file. + Comma-delimited files with a header line are now + permitted. + --covar-name <name...> : Only load the designated covariate(s) from the + --covar (if one was specified), --pheno (if no + --covar), or .psam (if no --covar or --pheno) + file. + --covar-col-nums <#...> : Only load the covariate(s) in the designated + column number(s) from the --covar (if one was + specified) or --pheno (if no --covar) file. + --within <f> [new pheno name] : Import a PLINK 1.x categorical phenotype. + (Phenotype name defaults to 'CATPHENO'.) + * If any numeric values are present, ALL + values must be numeric. In that case, 'C' + is added in front of all category names. + * 'NA' is treated as a missing value. + --mwithin <n> : Load --within categories from column n+2. + --family [new pheno name] : Create a categorical phenotype from FID. + Restrictions on and handling of numeric + values are the same as for --within. + --family-missing-catname <nm> : Make --family treat the specified FID as + missing. + --keep <fname...> : Exclude all samples not named in a file. + --remove <fname...> : Exclude all samples named in a file. + --keep-fam <fn...> : Exclude all families not named in a file. + --remove-fam <f...> : Exclude all families named in a file. + --extract [{bed0 | bed1}] <f...> : Usually excludes all variants (not) named + --exclude [{bed0 | bed1}] <f...> in the given file(s). When multiple files + are named, they are concatenated. + With the 'bed0' or 'bed1' modifier, + variants outside/inside the positional + ranges in the interval-BED file(s) are + excluded instead. 'bed0' tells PLINK 2 to + assume the interval bounds follow the UCSC + 0-based half-open convention, while 'bed1' + (equivalent to PLINK 1.9 'range') + specifies 1-based fully-closed. + --extract-intersect [{bed0 | bed1}] <f...> : Just like --extract, except that + a variant must be in the + intersection, rather than just + the union, of the files to + remain. + --keep-cats <filename> : These can be used individually or in combination + --keep-cat-names <nm...> to define a list of categories to keep; all + samples not in one of the named categories are + excluded. Use spaces to separate category names + for --keep-cat-names. Use the --missing-catname + value (default 'NONE') to refer to the group of + uncategorized samples. + --keep-cat-pheno <pheno> : If more than one categorical phenotype is loaded, + or you wish to filter on a categorical covariate, + --keep-cat-pheno must be used to specify which + phenotype/covariate --keep-cats and + --keep-cat-names apply to. + --remove-cats <filename> : Exclude all categories named in the file. + --remove-cat-names <...> : Exclude named categories. + --remove-cat-pheno <phe> : Specify pheno for --remove-cats/remove-cat-names. + --split-cat-pheno [{omit-most | omit-last}] ['covar-01'] + [cat. pheno/covar name(s)...] : + Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last') + binary phenotypes, with names of the form <orig. pheno name>=<cat. name>. + (As a consequence, affected phenotypes and categories are not permitted to + contain the '=' character.) + * This happens after all sample filters. + * If no phenotype or covariate names are provided, all categorical + phenotypes (but not covariates) are processed. + * By default, generated covariates are coded as 1=false, 2=true. To code + them as 0=false, 1=true instead, add the 'covar-01' modifier. + --loop-cats <pheno/covar> : Run variant filters and subsequent operations + on just the samples in the first category; then + just the samples in the second category; and so + on, for all categories in the named categorical + phenotype. + --no-id-header ['iid-only'] : Don't include a header line in .id output + files. This normally forces two-column FID/IID + output; add 'iid-only' to force just + single-column IID. + --variance-standardize [pheno/covar name(s)...] + --covar-variance-standardize [covar name(s)...] : + Linearly transform named covariates (and quantitative phenotypes, if + --variance-standardize) to mean-zero, variance 1. If no parameters are + provided, all possible phenotypes/covariates are affected. + This is frequently necessary to prevent multicollinearity when dealing with + covariates where abs(mean) is much larger than abs(standard deviation), + such as year of birth. + --quantile-normalize [...] : Force named covariates and quantitative + --pheno-quantile-normalize [...] phenotypes to a N(0,1) distribution, + --covar-quantile-normalize [...] preserving only the original rank orders. + --chr <chr(s)...> : Exclude all variants not on the given chromosome(s). + Valid choices for humans are 0 (unplaced), 1-22, X, Y, + XY, MT, PAR1, and PAR2. Separate multiple chromosomes + with spaces and/or commas, and use a dash (no adjacent + spaces permitted) to denote a range, e.g. + '--chr 1-4, 22, par1, x, par2'. + --not-chr <...> : Reverse of --chr (exclude variants on listed + chromosomes). + --autosome : Exclude all non-autosomal variants. + --autosome-par : Exclude all non-autosomal variants, except those in a + pseudo-autosomal region. + --snps-only ['just-acgt'] : Exclude non-SNP variants. By default, SNP = all + allele codes are single-character (so + multiallelic variants with a mix of SNPs and + non-SNPs are excluded; split your variants first + if that's a problem). + The 'just-acgt' modifier restricts SNP codes to + {A,C,G,T,a,c,g,t,<missing>}. + --from <var ID> : Use ID(s) to specify a variant range to load. When used + --to <var ID> together, both variants must be on the same chromosome. + (--snps can be used to specify intervals which cross + chromosome boundaries.) + --snp <var ID> : Specify a single variant to load. + --exclude-snp <ID> : Specify a single variant to exclude. + --window <kbs> : With --snp/--exclude-snp, loads/excludes all variants + within half the specified kb distance of the named one. + --from-bp <pos> : Use base-pair coordinates to define a variant range to + --to-bp <pos> load. + --from-kb <pos> * You must use these with --chr, specifying a single + --to-kb <pos> chromosome. + --from-mb <pos> * Decimals and negative numbers are permitted. + --to-mb <pos> * The --to-bp(/-kb/-mb) position is no longer permitted + to be smaller than the --from-bp position. + --snps <var IDs...> : Use IDs to specify variant range(s) to load or + --exclude-snps <...> exclude. E.g. '--snps rs1111-rs2222, rs3333, rs4444'. + --force-intersect : PLINK 2 normally errors out when multiple variant + inclusion filters (--extract, --extract-col-cond, + --extract-intersect, --from/--to, --from-bp/--to-bp, + --snp, --snps) are specified. --force-intersect + allows the run to proceed; the set intersection will + be taken. + --thin <p> : Randomly remove variants, retaining each with prob. p. + --thin-count <n> : Randomly remove variants until n of them remain. + --bp-space <bps> : Remove variants so that each pair is no closer than + the given bp distance. + --thin-indiv <p> : Randomly remove samples, retaining with prob. p. + --thin-indiv-count <n> : Randomly remove samples until n of them remain. + --keep-col-match <f> <val(s)...> : Exclude all samples without a 3rd column + entry in the given file exactly matching + one of the given strings. (Separate + multiple strings with spaces.) + --keep-col-match-name <col name> : Check column with given name instead. + --keep-col-match-num <n> : Check nth column instead. + --geno [val] [{dosage | hh-missing}] + --mind [val] [{dosage | hh-missing}] : + Exclude variants (--geno) and/or samples (--mind) with missing call + frequencies greater than a threshold (default 0.1). (Note that the default + threshold is only applied if --geno/--mind is invoked without a parameter; + when --geno/--mind is not invoked, no missing call frequency ceiling is + enforced at all. Other inclusion/exclusion default thresholds work the + same way.) + By default, when a dosage is present but a hardcall is not, the genotype is + treated as missing; add the 'dosage' modifier to treat this case as + nonmissing. Alternatively, you can use 'hh-missing' to also treat + heterozygous haploid calls as missing. + --require-pheno [name(s)...] : Remove samples missing any of the named + --require-covar [name(s)...] phenotype(s)/covariate(s). If no parameters + are provided, all phenotype(s)/covariate(s) + must be present. + --maf [freq] [mode] : Exclude variants with allele frequency lower than a + (alias: --min-af) threshold (default 0.01). By default, the nonmajor + allele frequency is used; the other supported modes + are 'nref' (non-reference), 'alt1', and 'minor' + (least frequent). bcftools freq:mode notation is + permitted. + --max-maf <freq> [mode] : Exclude variants with MAF greater than the + (alias: --max-af) threshold. + --mac <ct> [mode] : Exclude variants with allele dosage lower than the + (alias: --min-ac) given threshold. + --max-mac <ct> [mode] : Exclude variants with allele dosage greater than + (alias: --max-ac) the given threshold. + --maf-succ : Rule of succession allele frequency estimation (used in + EIGENSOFT). Given j observations of one allele and k + observations of the other for a biallelic variant, infer + allele frequencies of (j+1) / (j+k+2) and + (k+1) / (j+k+2), rather than the default j / (j+k) and + k / (j+k). + Note that this does not affect --freq's output. + --min-alleles <ct> : Exclude variants with fewer than the given # of alleles. + (When a variant has exactly one ALT allele, and it's + a missing-code, it's excluded by "--min-alleles 2".) + --max-alleles <ct> : Exclude variants with more than the given # of alleles. + --read-freq <file> : Load allele frequency estimates from the given --freq or + --geno-counts (or PLINK 1.9 --freqx) report, instead of + imputing them from the immediate dataset. + --hwe <p> ['midp'] ['keep-fewhet'] : + Exclude variants with Hardy-Weinberg equilibrium exact test p-values below + a threshold. + * By default, only founders are considered. + * chrX p-values are now computed using Graffelman and Weir's method. + * For variants with k alleles with k>2, k separate 'biallelic' tests are + performed, and the variant is filtered out if any of them fail. + * With 'keep-fewhet', variants which fail the test in the too-few-hets + direction are not excluded. On chrX, this uses the ratio between the + Graffelman/Weir p-value and the female-only p-value. + * There is currently no special handling of case/control phenotypes. + --mach-r2-filter [min] [max] : Exclude variants with MaCH imputation quality + metric less than min or greater than max + (defaults 0.1 and 2.0). (Monomorphic + variants, with r2 = nan, are not excluded.) + * This is NOT identical to the R2 metric + reported by Minimac3 0.1.13+; see below. + * If a single parameter is provided, it is + treated as the minimum. + * The metric is not computed on chrX and MT. + --minimac3-r2-filter <min> [max] : Compute Minimac3 R2 values from scratch, + and exclude variants with R2 less than min + or (if max is provided) greater than max. + * Note that this requires phased-dosage + data for all samples and variants; + otherwise this will systematically + underestimate imputation quality, since + unphased hardcalls/dosages are treated + as if they were maximally uncertain. + (Use --extract-if-info/--exclude-if-info + to filter on precomputed Minimac3 R2 in + a VCF/.pvar INFO column.) + --keep-females : Exclude male and unknown-sex samples. + --keep-males : Exclude female and unknown-sex samples. + --keep-nosex : Exclude all known-sex samples. + --remove-females : Exclude female samples. + --remove-males : Exclude male samples. + --remove-nosex : Exclude unknown-sex samples. + --keep-founders : Exclude nonfounder samples. + --keep-nonfounders : Exclude founder samples. + --keep-if <pheno/covar> <op> <val> : Exclude samples which don't/do satisfy a + --remove-if <pheno/covar> <op> <v> comparison predicate, e.g. + --keep-if "PHENO1 == case" + Unless the operator is !=, the predicate + always evaluates to false when the + phenotype/covariate is missing. + --nonfounders : Include nonfounders in allele freq/HWE calculations. + --bad-freqs : When PLINK 2 needs decent allele frequencies, it + normally errors out if they aren't provided by + --read-freq and less than 50 founders are available to + impute them from. Use --bad-freqs to force PLINK 2 to + proceed in this case. + --export-allele <file> : With --export A/A-transpose/AD, count alleles named + in the file, instead of REF alleles. + --output-chr <MT code> : Set chromosome coding scheme in output files by + providing the desired human mitochondrial code. + Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM', + and 'chrMT'; default is now 'MT' (note that this is + a change from PLINK 1.x, which defaulted to '26'). + --output-missing-genotype <ch> : Set the code used to represent missing + genotypes in output files (default '.'). + --output-missing-phenotype <s> : Set the string used to represent missing + phenotypes in output files (default 'NA'). + --sort-vars [mode] : Sort variants by chromosome, then position, then + ID. The following string orders are supported: + * 'natural'/'n': Natural sort (default). + * 'ascii'/'a': ASCII. + This must be used with --make-[b]pgen/--make-bed. + --set-hh-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set non-MT + heterozygous haploid hardcalls, and all + female chrY calls, to missing. (Unlike + PLINK 1.x, this treats unknown-sex chrY + genotypes like males, not females.) + By default, all associated dosages are + also erased; use 'keep-dosage' to keep + them all. + --set-mixed-mt-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set + mixed MT hardcalls to missing. + --split-par <bp1> <bp2> : Changes chromosome code of all X chromosome + --split-par <build> variants with bp position <= bp1 to PAR1, and those + with position >= bp2 to PAR2. The following build + codes are supported as shorthand: + * 'b36'/'hg18' = NCBI 36, 2709521/154584237 + * 'b37'/'hg19' = GRCh37, 2699520/154931044 + * 'b38'/'hg38' = GRCh38, 2781479/155701383 + --merge-par : Merge PAR1/PAR2 back with X. Requires PAR1 to be + positioned immediately before X, and PAR2 to be + immediately after X. (Should *not* be used with + "--export vcf", since it causes male + homozygous/missing calls in PAR1/PAR2 to be + reported as haploid.) + --merge-x : Merge XY back with X. This usually has to be + combined with --sort-vars. + --set-missing-var-ids <t> : Given a template string with a '@' where the + --set-all-var-ids <t> chromosome code should go and '#' where the bp + coordinate belongs, --set-missing-var-ids + assigns chromosome-and-bp-based IDs to unnamed + variants, while --set-all-var-ids resets all + IDs. + You may also use '$r'/'$a' to refer to the + ref and alt1 alleles, or '$1'/'$2' to refer to + them in alphabetical order. + --var-id-multi <t> : Specify alternative templates for multiallelic + --var-id-multi-nonsnp <t> variants. ('$a' and '$1'/'$2' should be avoided + here, though they're technically still allowed.) + --new-id-max-allele-len <len> [{error | missing | truncate}] : + Specify maximum number of leading characters from allele codes to include + in new variant IDs, and behavior on longer codes (defaults 23, error). + --missing-var-code <str> : Change unnamed variant code for --rm-dup, + --set-{missing|all}-var-ids, and + --recover-var-ids (default '.'). + --update-map <f> [bpcol] [IDcol] [skip] : Update variant bp positions. + --update-name <f> [newcol] [oldcol] [skip] : Update variant IDs. + --recover-var-ids <file> ['strict-bim-order'] [{rigid | force}] ['partial'] : + Undo --set-all-var-ids, given the original .pvar/VCF/.bim file. Original + IDs are looked up by position and allele codes. + * By default, if the original-ID file is a .bim, allele order is ignored. + Use 'strict-bim-order' to force A1=ALT, A2=REF. + * If any variant has multiple matching records in the original-ID file, and + the IDs conflict, --recover-var-ids writes the affected (current) ID(s) + to <output prefix>.recoverid.dup, and normally errors out. If the + original-ID file has the same number of variants in the same order, you + can still recover the old IDs with the 'rigid' modifier in this case. + Alternatively, to proceed and assign the missing-ID code to these + variants, add the 'force' modifier. (The .recoverid.dup file is still + written when 'rigid' or 'force' is specified.) + * --recover-var-ids normally expects to replace all variant IDs, and errors + out if any are left untouched. Add the 'partial' modifier when you + actually want to update just a proper subset. + --update-alleles <fname> : Update variant allele codes. + --update-ids <fname> : Update sample IDs. + --update-parents <fname> : Update parental IDs. + --update-sex <filename> ['col-num='<n>] ['male0'] : + Update sex information. + * By default, if there is a header line starting with '#FID'/'#IID', sex is + loaded from the first column titled 'SEX' (any capitalization); + otherwise, column 3 is assumed. Use 'col-num=' to force a column number. + * Only the first character in the sex column is processed. By default, + '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female, + and '0'/'N' is interpreted as unknown-sex. To change this to '0'/'M'/'m' + = male, '1'/'F'/'f' = female, anything else other than '2' = unknown-sex, + add 'male0'. + --real-ref-alleles : Treat A2 alleles in a PLINK 1.x fileset as actual REF + alleles; otherwise they're marked as provisional. + --maj-ref ['force'] : Set major alleles to reference, like PLINK 1.x + automatically did. (Note that this is now opt-in + rather than opt-out; --keep-allele-order is no longer + necessary to prevent allele-swapping.) + * This can only be used in runs with + --make-bed/--make-[b]pgen/--export and no other + commands. + * By default, this only affects variants marked as + having 'provisional' reference alleles. Add 'force' + to apply this to all variants. + * All new reference alleles are marked as provisional. + --ref-allele ['force'] <filename> [refcol] [IDcol] [skip] + --alt1-allele ['force'] <filename> [alt1col] [IDcol] [skip] : + These set the alleles specified in the file to ref (--ref-allele) or alt1 + (--alt1-allele). They can be combined in the same run. + * These can only be used in runs with --make-bed/--make-[b]pgen/--export + and no other commands. + * "--ref-allele <VCF filename> 4 3 '#'", which scrapes reference allele + assignments from a VCF file, is especially useful. + * By default, these error out when asked to change a 'known' reference + allele. Add 'force' to permit that (when e.g. switching to a new + reference genome). + * When --alt1-allele changes the previous ref allele to alt1, the previous + alt1 allele is set to reference and marked as provisional. + --ref-from-fa ['force'] : This sets reference alleles from the --fa file when + it can be done unambiguously (note that it's never + possible for deletions or some insertions). + By default, it errors out when asked to change a + 'known' reference allele; add the 'force' modifier + to permit that. + --normalize ['list'] : Left-normalize all variants, using the --fa file. + (alias: --norm) (Assumes no differences in capitalization.) The + 'list' modifier causes a list of affected variant + IDs to be written to <output prefix>.normalized. + --indiv-sort <mode> [f] : Specify sample ID sort order for merge and + --make-[b]pgen/--make-bed. The following four + modes are supported: + * 'none'/'0' keeps samples in the order they were + loaded. Default for non-merge. + * 'natural'/'n' invokes "natural sort", e.g. + 'id2' < 'ID3' < 'id10'. Default when merging. + * 'ascii'/'a' sorts in ASCII order, e.g. + 'ID3' < 'id10' < 'id2'. + * 'file'/'f' uses the order in the given file + (named in the last parameter). + --king-table-filter <min> : Specify minimum kinship coefficient for + inclusion in --make-king-table report. + --king-table-subset <f> [kmin] : Restrict current --make-king-table run to + sample pairs listed in the given .kin0 file. + If a second parameter is provided, only + sample pairs with kinship >= that threshold + (in the input .kin0) are processed. + --condition <variant ID> [{dominant | recessive}] ['multiallelic'] + --condition-list <fname> [{dominant | recessive}] ['multiallelic'] : + Add the given variant, or all variants in the given file, as --glm + covariates. + By default, this errors out if any of the variants are multiallelic; add + the 'multiallelic' ('m' for short) modifier to allow them. They'll + effectively be split against the major allele (unless --glm's 'omit-ref' + modifier was specified), and all induced covariate names--even for + biallelic variants--will have an underscore followed by the allele code at + the end. + --parameters <...> : Include only the given covariates/interactions in the + --glm model, identified by a list of 1-based indices + and/or ranges of them. + --tests <...> : Perform a (joint) test on the specified term(s) in the + --tests all --glm model, identified by 1-based indices and/or ranges + of them. + * Note that, when --parameters is also present, the + indices refer to the terms remaining AFTER pruning by + --parameters. + * You can use '--tests all' to include all terms. + --vif <max VIF> : Set VIF threshold for --glm multicollinearity check + (default 50). (This is no longer skipped for + case/control phenotypes.) + --max-corr <val> : Skip --glm regression when the absolute value of the + correlation between two predictors exceeds this value + (default 0.999). + --xchr-model <m> : Set the chrX --glm/--condition[-list]/--[v]score model. + * '0' = skip chrX. + * '1' = add sex as a covar on chrX, code males 0..1. + * '2' (default) = chrX sex covar, code males 0..2. + (Use the --glm 'interaction' modifier to test for + interaction between genotype and sex.) + --adjust ['zs'] ['gc'] ['log10'] ['cols='<column set descriptor>] : + For each association test in this run, report some basic multiple-testing + corrections, sorted in increasing-p-value order. Modifiers work the same + way as they do on --adjust-file. + --lambda : Set genomic control lambda for --adjust[-file]. + --adjust-chr-field <n...> : Set --adjust-file input field names. When + --adjust-pos-field <n...> multiple parameters are given to these flags, + --adjust-id-field <n...> earlier names take precedence over later ones. + --adjust-ref-field <n...> + --adjust-alt-field <n...> + --adjust-a1-field <n...> + --adjust-test-field <n...> + --adjust-p-field <n...> + --ci <size> : Report confidence ratios for odds ratios/betas. + --pfilter <val> : Filter out assoc. test results with higher p-values. + --score-col-nums <...> : Process all the specified coefficient columns in the + --score file, identified by 1-based indexes and/or + ranges of them. + --q-score-range <range file> <data file> [i] [j] ['header'] ['min'] : + Apply --score to subset(s) of variants in the primary score list(s) based + on e.g. p-value ranges. + * The first file should have range labels in the first column, p-value + lower bounds in the second column, and upper bounds in the third column. + Lines with too few entries, or nonnumeric values in the second or third + column, are ignored. + * The second file should contain a variant ID and a p-value on each line + (except possibly the first). Variant IDs are read from column #i and + p-values are read from column #j, where i defaults to 1 and j defaults to + i+1. The 'header' modifier causes the first nonempty line of this file + to be skipped. + * By default, --q-score-range errors out when a variant ID appears multiple + times in the data file (and is also present in the main dataset). To use + the minimum p-value in this case instead, add the 'min' modifier. + --vscore-col-nums <...> : Process all the specified coefficient columns in + the --variant-score file, identified by 1-based + indexes and/or ranges of them. + --parallel <k> <n> : Divide the output matrix into n pieces, and only compute + the kth piece. The primary output file will have the + piece number included in its name, e.g. plink2.king.13 + or plink2.king.13.zst if k is 13. Concatenating these + files in order will yield the full matrix of interest. + (Yes, this can be done before decompression.) + N.B. This generally cannot be used to directly write a + symmetric square matrix. Choose square0 or triangle + shape instead, and postprocess as necessary. + --memory <val> ['require'] : Set size, in MiB, of initial workspace malloc + attempt. To error out instead of reducing the + request size when the initial attempt fails, add + the 'require' modifier. + --threads <val> : Set maximum number of compute threads. + --d <char> : Change variant/covariate range delimiter (normally '-'). + --seed <val...> : Set random number seed(s). Each value must be an + integer between 0 and 4294967295 inclusive. + Note that --threads and "--memory require" may also be + needed to reproduce some randomized runs. + --output-min-p <p> : Specify minimum p-value to write to reports. (2.23e-308 + is useful for preventing underflow in some programs.) + --debug : Use slower, more crash-resistant logging method. + --randmem : Randomize initial workspace memory (helps catch + uninitialized-memory bugs). + --warning-errcode : Return a nonzero error code to the OS when a run + completes with warning(s). + --zst-level <lvl> : Set the Zstd compression level (1-22, default 3). + + Primary methods paper: + Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015) + Second-generation PLINK: rising to the challenge of larger and richer datasets. + GigaScience, 4. + + + + ]]></help> + <citations> + <citation type="doi">10.1186/s13742-015-0047-8</citation> + <citation type="bibtex">@ARTICLE{Blankenberg20-plink, + author = {Daniel Blankenberg Lab, et al}, + title = {In preparation..}, + }</citation> + </citations> +</tool>