Mercurial > repos > iuc > bcftools_convert_from_vcf
diff bcftools_convert_from_vcf.xml @ 25:61d4b20f3b11 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
| author | iuc |
|---|---|
| date | Tue, 02 Dec 2025 07:43:16 +0000 |
| parents | 0155f20adc71 |
| children |
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--- a/bcftools_convert_from_vcf.xml Sun Aug 18 09:47:32 2024 +0000 +++ b/bcftools_convert_from_vcf.xml Tue Dec 02 07:43:16 2025 +0000 @@ -4,12 +4,10 @@ <token name="@EXECUTABLE@">convert</token> <import>macros.xml</import> <xml name="macro_vcf_ids"> - <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" - label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/> + <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/> </xml> <xml name="macro_haploid2diploid"> - <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" - label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/> + <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/> </xml> <xml name="macro_sexinfo"> <conditional name="sex_info"> @@ -28,7 +26,7 @@ <param name="sex_info_file" type="data" format="tabular" label="per sample sex designation file"/> </when> <when value="entry"> - <param name="sex_info_lines" type="text" area="True" label="per sample sex designation" > + <param name="sex_info_lines" type="text" area="True" label="per sample sex designation"> <validator type="regex" message="sample M or F separated by TAB">^(\S+[ \t][MF](\n\S+[ \t][MF])*)$</validator> <sanitizer sanitize="False"/> </param> @@ -43,11 +41,10 @@ #end if </token> </macros> - <expand macro="bio_tools" /> - <expand macro="requirements" /> - <expand macro="version_command" /> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @@ -81,7 +78,7 @@ ## Primary Input/Outputs -"$input_file" . +@INPUT_FILE@ . ]]> </command> <configfiles> @@ -91,15 +88,15 @@ #end if]]></configfile> </configfiles> <inputs> - <expand macro="macro_input" /> + <expand macro="macro_input"/> <section name="sec_restrict" expanded="false" title="Restrict to"> - <expand macro="macro_restrict" /> - <expand macro="macro_restrict" type="target" label_type="Target" /> - <expand macro="macro_samples" /> - <expand macro="macro_include" /> - <expand macro="macro_exclude" /> + <expand macro="macro_region_restrict"/> + <expand macro="macro_target_restrict"/> + <expand macro="macro_samples"/> + <expand macro="macro_include"/> + <expand macro="macro_exclude"/> </section> - <param argument="--keep-duplicates" type="boolean" truevalue="--keep-duplicates" falsevalue="" checked="false" label="Keep duplicates" help="Keep all multiallelic variants" /> + <param argument="--keep-duplicates" type="boolean" truevalue="--keep-duplicates" falsevalue="" checked="false" label="Keep duplicates" help="Keep all multiallelic variants"/> <conditional name="convert"> <param name="convert_to" type="select" label="convert to"> <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option> @@ -115,7 +112,7 @@ <option value="GL">GL</option> --> </param> - <param name="convert_3N6" argument="--3N6" type="boolean" truevalue="--3N6" falsevalue="" checked="false" label="3N6 format" help="Use 3N+6 column format instead of the old 3N+5 column format" /> + <param name="convert_3N6" argument="--3N6" type="boolean" truevalue="--3N6" falsevalue="" checked="false" label="3N6 format" help="Use 3N+6 column format instead of the old 3N+5 column format"/> <expand macro="macro_vcf_ids"/> <expand macro="macro_sexinfo"/> </when> @@ -133,20 +130,22 @@ </inputs> <outputs> <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen"> - <filter>convert['convert_to'] == 'gen_sample'</filter> + <filter>convert['convert_to'] == 'gen_sample'</filter> </data> <data name="output_hap" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.haps"> - <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter> + <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter> </data> <data name="output_legend" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.legend"> - <filter>convert['convert_to'] == 'hap_legend_sample'</filter> + <filter>convert['convert_to'] == 'hap_legend_sample'</filter> </data> <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/> </outputs> <tests> <test expect_num_outputs="2"> - <param name="input_file" ftype="vcf" value="convert.vcf" /> - <param name="convert_to" value="gen_sample" /> + <param name="input_file" ftype="vcf" value="convert.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="gen_sample"/> + </conditional> <output name="output_gen"> <assert_contents> <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/> @@ -159,10 +158,12 @@ </output> </test> <test expect_num_outputs="2"> - <param name="input_file" ftype="vcf" value="convert.vcf" /> - <param name="convert_to" value="gen_sample" /> - <param name="tag" value="GP" /> - <param name="convert_3N6" value="True" /> + <param name="input_file" ftype="vcf" value="convert.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="gen_sample"/> + <param name="tag" value="GP"/> + <param name="convert_3N6" value="True"/> + </conditional> <output name="output_gen"> <assert_contents> <has_text text="X:2698630_A_G X:2698630_A_G 2698630 A G 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000"/> @@ -170,11 +171,13 @@ </output> </test> <test expect_num_outputs="2"> - <param name="input_file" ftype="vcf" value="check.vcf" /> - <param name="convert_to" value="gen_sample" /> - <param name="tag" value="GT" /> - <param name="convert_3N6" value="True" /> - <param name="vcf_ids" value="True" /> + <param name="input_file" ftype="vcf" value="check.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="gen_sample"/> + <param name="tag" value="GT"/> + <param name="convert_3N6" value="True"/> + <param name="vcf_ids" value="True"/> + </conditional> <output name="output_gen"> <assert_contents> <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/> @@ -182,8 +185,10 @@ </output> </test> <test expect_num_outputs="2"> - <param name="input_file" ftype="vcf" value="convert.vcf" /> - <param name="convert_to" value="hap_sample" /> + <param name="input_file" ftype="vcf" value="convert.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="hap_sample"/> + </conditional> <output name="output_hap"> <assert_contents> <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> @@ -191,8 +196,10 @@ </output> </test> <test expect_num_outputs="3"> - <param name="input_file" ftype="vcf" value="convert.vcf" /> - <param name="convert_to" value="hap_legend_sample" /> + <param name="input_file" ftype="vcf" value="convert.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="hap_legend_sample"/> + </conditional> <output name="output_hap"> <assert_contents> <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> @@ -212,8 +219,10 @@ </test> <!-- Test keep-duplicates option --> <test expect_num_outputs="3"> - <param name="input_file" ftype="vcf" value="convert.vcf" /> - <param name="convert_to" value="hap_legend_sample" /> + <param name="input_file" ftype="vcf" value="convert.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="hap_legend_sample"/> + </conditional> <param name="keep_duplicates" value="true"/> <output name="output_hap"> <assert_contents> @@ -232,15 +241,22 @@ </assert_contents> </output> <assert_command> - <has_text text="--keep-duplicates" /> + <has_text text="--keep-duplicates"/> </assert_command> </test> <!-- Test region overlap --> <test expect_num_outputs="2"> - <param name="input_file" ftype="vcf" value="convert.vcf" /> - <param name="convert_to" value="gen_sample" /> + <param name="input_file" ftype="vcf" value="convert.vcf"/> + <conditional name="convert"> + <param name="convert_to" value="gen_sample"/> + </conditional> <section name="sec_restrict"> - <param name="regions_overlap" value="1"/> + <conditional name="regions"> + <param name="regions_src" value="regions" /> + <repeat name="region_specs"> + <param name="chrom" value="X" /> + </repeat> + </conditional> </section> <output name="output_gen"> <assert_contents> @@ -253,11 +269,10 @@ </assert_contents> </output> <assert_command> - <has_text text="--regions-overlap" /> + <has_text text="--regions-overlap"/> </assert_command> </test> </tests> - <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ from vcf @@ -271,8 +286,8 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ -@BCFTOOLS_WIKI@ +@BCFTOOLS_HOWTOS@ ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>