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changeset 0:8a482a9aa45d draft

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Uploaded
author devteam
date Thu, 19 Mar 2015 12:42:11 -0400
parents
children 834e1f313036
files macros.xml test-data/vcfannotate.bed test-data/vcfbedintersect-test1.vcf test-data/vcfbedintersect-test2.vcf test-data/vcflib.vcf tool_dependencies.xml vcfbedintersect.xml
diffstat 7 files changed, 220 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Mar 19 12:42:11 2015 -0400
@@ -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/vcfannotate.bed	Thu Mar 19 12:42:11 2015 -0400
@@ -0,0 +1,46 @@
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+20	853296	896960	uc010zpn.2	0	-	853750	896839	0	8	467,167,102,116,248,122,156,412,	0,5507,7093,8517,12424,15664,17559,43252,
+20	939095	982907	uc002wej.3	0	-	940999	982807	0	5	2014,186,141,189,179,	0,5482,8721,9497,43633,
+20	939095	982907	uc002wek.3	0	-	940999	982807	0	4	2014,141,189,179,	0,8721,9497,43633,
+20	1093905	1147970	uc010zpo.2	0	+	1106275	1146898	0	7	147,153,83,186,54,159,1100,	0,12235,14163,21858,49868,51056,52965,
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+20	1099239	1148426	uc002wen.4	0	+	1099416	1145724	0	7	306,153,83,186,54,159,2754,	0,6901,8829,16524,44534,45722,46433,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfbedintersect-test1.vcf	Thu Mar 19 12:42:11 2015 -0400
@@ -0,0 +1,23 @@
+##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
+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:.,.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfbedintersect-test2.vcf	Thu Mar 19 12:42:11 2015 -0400
@@ -0,0 +1,24 @@
+##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
+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:.,.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib.vcf	Thu Mar 19 12:42:11 2015 -0400
@@ -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	Thu Mar 19 12:42:11 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfbedintersect.xml	Thu Mar 19 12:42:11 2015 -0400
@@ -0,0 +1,62 @@
+<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3">
+  <description>Intersect VCF and BED datasets</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>
+    #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
+        vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
+   #else:
+        vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
+   #end if
+
+  </command>
+  <inputs>
+    <!-- selecting refernce source -->
+    <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
+     <conditional name="bed_vs_interval">
+       <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
+	 <option value="bed">BED</option>
+	 <option value="interval">Interval</option>
+       </param>
+       <when value="bed">
+	 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
+       </when>
+       <when value="interval">
+	 <param name="int_input" type="text" size="20" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
+       </when>
+     </conditional>
+     <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="bed_vs_interval_selector" value="bed" />
+      <param name="bed_input" value="vcfannotate.bed" />
+      <param name="invert" value="False" />
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
+    </test>
+    <test>
+      <param name="bed_vs_interval_selector" value="interval" />
+      <param name="int_input" value="20:1-30000" />
+      <param name="invert" value="False" />
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
+    </test>
+    </tests>
+
+  <help>
+
+Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).
+
+----                                                                                                                                                                              
+
+VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).     
+</help>
+  <expand macro="citations" />
+</tool>