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changeset 0:a9ce47a1d653 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:30:48 -0500
parents
children 0b93ada8f718
files macros.xml test-data/vcfcombine-test1.vcf test-data/vcflib.vcf tool_dependencies.xml vcfcombine.xml
diffstat 5 files changed, 136 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Nov 09 12:30:48 2015 -0500
@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+    </xml>
+   	<xml name="citations">
+   	     <citations>
+             <citation type="bibtex">
+@misc{Garrison2015,
+  author = {Garrison, Erik},
+  year = {2015},
+  title = {vcflib},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/ekg/vcflib},
+}
+             </citation>
+   	     </citations>
+   	</xml>
+    <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfcombine-test1.vcf	Mon Nov 09 12:30:48 2015 -0500
@@ -0,0 +1,31 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
+##ALT=<ID=CNV,Description="Copy number variable region">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
+19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
+20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
+20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
+20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
+20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	0	.	.	GT	0/0	0|0	.
+X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib.vcf	Mon Nov 09 12:30:48 2015 -0500
@@ -0,0 +1,31 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
+##ALT=<ID=CNV,Description="Copy number variable region">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
+19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
+20	1234567	microsat1	G	GA,GAC	50	PASS	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	.	.	.	GT	0/0	0|0	./.
+X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Nov 09 12:30:48 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="3ac0905f7b7c" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfcombine.xml	Mon Nov 09 12:30:48 2015 -0500
@@ -0,0 +1,40 @@
+<tool id="vcfcombine" name="VCFcombine:" version="0.0.4">
+  <description>Combine multiple VCF datasets</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>
+
+   vcfcombine
+
+   #for $input_vcf in $input_vcfs:
+        "${input_vcf}"
+   #end for
+
+   > "${out_file1}"
+
+  </command>
+  <inputs>
+    <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_vcfs" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfcombine-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted.
+
+-----
+
+Vcfcombine @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>