# HG changeset patch
# User iuc
# Date 1455620073 18000
# Node ID 386b3e7c2f77f04a28d749be277f517746df2294
# Parent  a4e8364eb115d4da919ced9393d144a967390c99
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty

diff -r a4e8364eb115 -r 386b3e7c2f77 gemini_load.xml
--- a/gemini_load.xml	Tue Dec 29 11:06:57 2015 -0500
+++ b/gemini_load.xml	Tue Feb 16 05:54:33 2016 -0500
@@ -15,12 +15,12 @@
 
         gemini
             #if $annotation_databases:
-                --annotation-dir ${annotation_databases.fields.path}
+                --annotation-dir "${annotation_databases.fields.path}"
             #end if
             @BINARY@
             -v input.vcf.gz
             #if str( $annotation_type ) != "None":
-                -t $annotation_type
+                -t "$annotation_type"
             #end if
 
             #if $ped:
@@ -33,7 +33,7 @@
             $no_load_genotypes
             $no_genotypes
             $passonly
-            $infostring
+            "$infostring"
             --cores \${GALAXY_SLOTS:-4}
 
             "${ outfile }"
diff -r a4e8364eb115 -r 386b3e7c2f77 gemini_macros.xml
--- a/gemini_macros.xml	Tue Dec 29 11:06:57 2015 -0500
+++ b/gemini_macros.xml	Tue Feb 16 05:54:33 2016 -0500
@@ -60,6 +60,7 @@
                     <option value="alt">alt</option>
                     <option value="impact">impact</option>
                     <option value="impact_severity">impact_severity</option>
+                    <option value="max_aaf_all">alternative allele frequency</option>
                 </param>
             </when>
         </conditional>
@@ -111,10 +112,8 @@
     </xml>
 
     <xml name="min_sequence_depth">
-        <param name="d" type="integer" value="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
-                help="default: 0 (-d)">
-            <validator type="in_range" min="0"/>
-        </param>
+        <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
+                help="default: 0 (-d)" />
     </xml>
 
     <xml name="min_gq">
@@ -124,11 +123,9 @@
     </xml>
 
     <xml name="gt_pl_max">
-        <param name="gt_pl_max" type="integer" value="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)">
-            <validator type="in_range" min="-1"/>
-        </param>
+        <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />
     </xml>
-    <token name="@VERSION@">0.18.0</token>
+    <token name="@VERSION@">0.18.1</token>
 
     <xml name="citations">
         <citations>
diff -r a4e8364eb115 -r 386b3e7c2f77 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Dec 29 11:06:57 2015 -0500
+++ b/repository_dependencies.xml	Tue Feb 16 05:54:33 2016 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="b68b5cd8b58a" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="eb54ffdea8a0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_actionable_mutations_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_actionable_mutations_result.tabular	Tue Feb 16 05:54:33 2016 -0500
@@ -0,0 +1,1 @@
+tum_name	chrom	start	end	ref	alt	gene	impact	is_somatic	in_cosmic_census	dgidb_info
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_amend_input.db
Binary file test-data/gemini_amend_input.db has changed
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_amend_input.ped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_amend_input.ped	Tue Feb 16 05:54:33 2016 -0500
@@ -0,0 +1,5 @@
+#family_id name paternal_id maternal_id sex phenotype ethnicity hair_color
+1 M10475    None None  1    1    None	brown
+1 M10478     M10475  M10500    2    2    None	red
+1 M10500     None    None    2    2    None	
+1 M128215    M10475  M10500    1    1    None	green
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_amend_result.db
Binary file test-data/gemini_amend_result.db has changed
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_dump_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_dump_result.tabular	Tue Feb 16 05:54:33 2016 -0500
@@ -0,0 +1,97 @@
+chrom	start	end	ref	alt	type	sub_type	aaf	in_dbsnp	gene	sample	genotype
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_1	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_2	G/G
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_2	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_2	G/G
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_1	G/G
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_1	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_3	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_3	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_3	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 child_4	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 dad_4	G/A
+chr1	16976	16977	G	A	snp	ts	0.375	0	DDX11L1 mom_4	G/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_1	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_2	A/G
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_2	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_2	A/G
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_1	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_1	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_3	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_3	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_3	A/G
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 child_4	A/G
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 dad_4	A/A
+chr1	17221	17222	A	G	snp	ts	0.166666666667	1	DDX11L1 mom_4	A/A
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_1	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_2	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_2	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_2	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_1	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_1	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_3	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_3	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_3	TTCT/TTCT
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P child_4	TTCT/T
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P dad_4	TTCT/T
+chr1	17362	17366	TTCT	T	indel	del	0.0833333333333	0	WASH7P mom_4	TTCT/TTCT
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_1	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_2	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_2	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_2	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_1	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_1	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_3	G/A
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_3	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_3	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 child_4	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 dad_4	G/G
+chr1	17562	17563	G	A	snp	ts	0.0416666666667	0	DDX11L1 mom_4	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_1	G/C
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_2	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_2	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_2	G/C
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_1	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_1	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_3	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_3	G/C
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_3	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 child_4	G/C
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 dad_4	G/G
+chr1	17696	17697	G	C	snp	tv	0.166666666667	1	DDX11L1 mom_4	G/G
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_1	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_2	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_2	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_2	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_1	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_1	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_3	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_3	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_3	A/A
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 child_4	A/G
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 dad_4	A/G
+chr1	17721	17722	A	G	snp	ts	0.125	1	DDX11L1 mom_4	A/G
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_1	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_2	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_2	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_2	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_1	C/A
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_1	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_3	C/A
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_3	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_3	C/C
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P child_4	C/A
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P dad_4	C/A
+chr1	17729	17730	C	A	snp	tv	0.208333333333	0	WASH7P mom_4	C/A
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_1	A/A
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_2	A/A
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_2	A/A
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_2	A/A
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_1	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_1	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_3	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_3	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_3	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 child_4	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 dad_4	A/G
+chr1	17745	17746	A	G	snp	ts	0.333333333333	1	DDX11L1 mom_4	A/G
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_fusions_result.tabular
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_gene_wise_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_gene_wise_result.tabular	Tue Feb 16 05:54:33 2016 -0500
@@ -0,0 +1,6 @@
+chrom	start	end	gene	impact	impact_severity	max_aaf_all	variant_filters	n_gene_variants	gene_filters
+chr10	48003991	48003992	ASAH2C	missense_variant	MED	0.543088975937	1	1	1
+chr10	126678091	126678092	CTBP2	stop_gained	HIGH	0.0904917363803	1	1	1
+chr10	135369531	135369532	SYCE1	missense_variant	MED	0.2698	1	1	1
+chr10	1142207	1142208	WDR37	stop_lost	HIGH	1.0	1	1	1
+chr16	72057434	72057435	DHODH	missense_variant	MED	0.000432002764818	1	1	1
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_is_somatic_result.db
Binary file test-data/gemini_is_somatic_result.db has changed
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_mendel_errors_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_mendel_errors_result.tabular	Tue Feb 16 05:54:33 2016 -0500
@@ -0,0 +1,10 @@
+chrom	start	end	vcf_id	variant_id	anno_id	ref	alt	qual	filter	type	sub_type	call_rate	in_dbsnp	rs_ids	sv_cipos_start_left	sv_cipos_end_left	sv_cipos_start_right	sv_cipos_end_right	sv_length	sv_is_precise	sv_tool	sv_evidence_type	sv_event_id	sv_mate_id	sv_strand	in_omim	clinvar_sig	clinvar_disease_name	clinvar_dbsource	clinvar_dbsource_id	clinvar_origin	clinvar_dsdb	clinvar_dsdbid	clinvar_disease_acc	clinvar_in_locus_spec_db	clinvar_on_diag_assay	clinvar_causal_allele	pfam_domain	cyto_band	rmsk	in_cpg_island	in_segdup	is_conserved	gerp_bp_score	gerp_element_pval	num_hom_ref	num_het	num_hom_alt	num_unknown	aaf	hwe	inbreeding_coeff	pi	recomb_rate	gene	transcript	is_exonic	is_coding	is_splicing	is_lof	exon	codon_change	aa_change	aa_length	biotype	impact	impact_so	impact_severity	polyphen_pred	polyphen_score	sift_pred	sift_score	anc_allele	rms_bq	cigar	depth	strand_bias	rms_map_qual	in_hom_run	num_mapq_zero	num_alleles	num_reads_w_dels	haplotype_score	qual_depth	allele_count	allele_bal	in_hm2	in_hm3	is_somatic	somatic_score	in_esp	aaf_esp_ea	aaf_esp_aa	aaf_esp_all	exome_chip	in_1kg	aaf_1kg_amr	aaf_1kg_eas	aaf_1kg_sas	aaf_1kg_afr	aaf_1kg_eur	aaf_1kg_all	grc	gms_illumina	gms_solid	gms_iontorrent	in_cse	encode_tfbs	encode_dnaseI_cell_count	encode_dnaseI_cell_list	encode_consensus_gm12878	encode_consensus_h1hesc	encode_consensus_helas3	encode_consensus_hepg2	encode_consensus_huvec	encode_consensus_k562	vista_enhancers	cosmic_ids	info	cadd_raw	cadd_scaled	fitcons	in_exac	aaf_exac_all	aaf_adj_exac_all	aaf_adj_exac_afr	aaf_adj_exac_amr	aaf_adj_exac_eas	aaf_adj_exac_fin	aaf_adj_exac_nfe	aaf_adj_exac_oth	aaf_adj_exac_sas	exac_num_het	exac_num_hom_alt	exac_num_chroms	max_aaf_all	gts	gt_types	gt_phases	gt_depths	gt_ref_depths	gt_alt_depths	gt_quals	gt_copy_numbers	gt_phred_ll_homref	gt_phred_ll_het	gt_phred_ll_homalt	family_id	family_members	family_genotypes	samples	family_count	violation	violation_prob
+chr10	1142207	1142208	None	1	4	T	C	3404.30004883	None	snp	ts	1.0	1	rs10794716	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10p15.3	None	0	0	0	None	None	7	1	1	0	0.166666666667	0.0718606383197	0.6	0.294117647059	0.200924	WDR37	ENST00000381329	1	1	0	1	exon_10_1142110_1142566	Tga/Cga	*250R	249	protein_coding	stop_lost	stop_lost	HIGH	None	None	None	None	None	None	None	122	None	36.0	0	0	8	0.0	2.67470002174	27.8999996185	8	None	None	None	None	None	1	0.999534883721	0.975034044485	0.991234814701	0	1	0.9942	1	1	0.9561	1	0.98762	None	None	None	None	0	None	2	Osteobl;Progfib	T	T	T	T	T	T	None	None	None	None	None	0.156188	1	0.997	0.997067786838	0.970305592927	0.998358956642	1	1	0.999595432887	0.998898678414	1	346	60354	121410	1.0	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C']	[0 0 1 0 0 0 0 0 3]	[False False False False False False False False False]	[38 29 23 38 29 22 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 22 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	2	plausible de novo;implausible de novo	0.00000
+chr10	1142207	1142208	None	1	4	T	C	3404.30004883	None	snp	ts	1.0	1	rs10794716	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10p15.3	None	0	0	0	None	None	7	1	1	0	0.166666666667	0.0718606383197	0.6	0.294117647059	0.200924	WDR37	ENST00000381329	1	1	0	1	exon_10_1142110_1142566	Tga/Cga	*250R	249	protein_coding	stop_lost	stop_lost	HIGH	None	None	None	None	None	None	None	122	None	36.0	0	0	8	0.0	2.67470002174	27.8999996185	8	None	None	None	None	None	1	0.999534883721	0.975034044485	0.991234814701	0	1	0.9942	1	1	0.9561	1	0.98762	None	None	None	None	0	None	2	Osteobl;Progfib	T	T	T	T	T	T	None	None	None	None	None	0.156188	1	0.997	0.997067786838	0.970305592927	0.998358956642	1	1	0.999595432887	0.998898678414	1	346	60354	121410	1.0	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C']	[0 0 1 0 0 0 0 0 3]	[False False False False False False False False False]	[38 29 23 38 29 22 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 22 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	T/T,T/T,C/C	3_kid	2	plausible de novo;implausible de novo	0.00000
+chr10	48003991	48003992	None	2	1	C	T	1047.86999512	None	snp	ts	1.0	1	rs142685947,rs3739968	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	1	None	3.10871e-42	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	1	0.3112	0.4573	0.3855	0.1241	0.5149	0.346645	grc_fix	73.3	40.3	92.8	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.553676	1	0.443	0.448537771896	0.288974151858	0.281426746944	0.543088975937	0.524984286612	0.478147713207	0.463529411765	0.418641164716	17495	15317	107302	0.543088975937	['C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T' 'C/T' 'C/T' 'C/T']	[1 1 3 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	C/C,C/C,C/T	2_kid	1	plausible de novo	0.00000
+chr10	48004991	48004992	None	3	1	C	T	1047.86999512	None	snp	ts	1.0	0	None	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	0	None	None	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	0	None	None	None	None	None	None	grc_fix	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.061011	0	None	None	None	None	None	None	None	None	None	None	None	None	-1.0	['C/T' 'C/T' 'C/T' 'C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T']	[1 1 1 1 1 3 0 0 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	C/C,C/C,C/T	3_kid	1	plausible de novo	0.00000
+chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	G/G,G/G,G/A	1_kid	2	plausible de novo;plausible de novo	0.00000
+chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	G/G,G/G,G/A	2_kid	2	plausible de novo;plausible de novo	0.00000
+chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	3	plausible de novo;plausible de novo;plausible de novo	0.00000
+chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	T/T,T/T,T/C	3_kid	3	plausible de novo;plausible de novo;plausible de novo	0.00000
+chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	T/T,T/T,T/C	2_kid	3	plausible de novo;plausible de novo;plausible de novo	0.00000
diff -r a4e8364eb115 -r 386b3e7c2f77 test-data/gemini_qc_result.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_qc_result.tabular	Tue Feb 16 05:54:33 2016 -0500
@@ -0,0 +1,5 @@
+sample	sex	chrX_homref	chrX_het	chrX_homalt	chrX_unknown
+M10475	male	0	0	0	0
+M10478	female	0	0	0	0
+M10500	female	0	0	0	0
+M128215	male	0	0	0	0
diff -r a4e8364eb115 -r 386b3e7c2f77 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 29 11:06:57 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 16 05:54:33 2016 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="gemini" version="0.18.1">
-        <repository changeset_revision="4afa532941cb" name="package_gemini_0_18_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="13ce32ffda3a" name="package_gemini_0_18_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>