| Previous changeset 0:88fd8ef7e4af (2015-03-19) Next changeset 2:958b6484a7f1 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfselectsamples commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml test-data/vcfselectsamples-test1.vcf vcfselectsamples.xml |
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removed:
tool_dependencies.xml |
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| diff -r 88fd8ef7e4af -r 43cecdfe7107 macros.xml --- a/macros.xml Thu Mar 19 14:45:17 2015 -0400 +++ b/macros.xml Thu Sep 15 16:07:06 2016 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="8a5602bf07">vcflib</requirement> + <requirement type="package" version="1.0.0_rc1">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,6 +10,7 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> + <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> <xml name="citations"> <citations> <citation type="bibtex"> |
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| diff -r 88fd8ef7e4af -r 43cecdfe7107 test-data/vcfselectsamples-test1.vcf --- a/test-data/vcfselectsamples-test1.vcf Thu Mar 19 14:45:17 2015 -0400 +++ b/test-data/vcfselectsamples-test1.vcf Thu Sep 15 16:07:06 2016 -0400 |
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| @@ -27,5 +27,5 @@ 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0/0:61:2:.,. 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 1/1:40:3 -20 1235237 . T . 0 . . GT 0/0 . +20 1235237 . T . 0 . . GT 0/0 ./. X 10 rsTest AC A,ATG 10 PASS . GT 0 0|2 |
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| diff -r 88fd8ef7e4af -r 43cecdfe7107 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 19 14:45:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?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> |
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| diff -r 88fd8ef7e4af -r 43cecdfe7107 vcfselectsamples.xml --- a/vcfselectsamples.xml Thu Mar 19 14:45:17 2015 -0400 +++ b/vcfselectsamples.xml Thu Sep 15 16:07:06 2016 -0400 |
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| @@ -1,53 +1,53 @@ -<tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.3"> - <description>Select samples from a VCF dataset</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset" /> - <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true"> - <options> - <filter type="data_meta" ref="input1" key="sample_names" /> - </options> -</param> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="vcf_samples" value="NA00001,NA00003"/> - <param name="input1" value="vcflib.vcf"/> - <output name="out_file1" file="vcfselectsamples-test1.vcf"/> - </test> - </tests> - <help> - -Allows to keep or remove samples from a VCF file. - ------ - -.. class:: infomark - - -**Example**: - -Selecting *NA00001* and *NA00003* from the following VCF line:: - - #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 - 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. - -will, obviously, remove *NA00002*:: - - #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003 - 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,. - ----- - -Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfselectsamples" name="VCFselectsamples:" version="@WRAPPER_VERSION@.0"> + <description>Select samples from a VCF dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset" /> + <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true"> + <options> + <filter type="data_meta" ref="input1" key="sample_names" /> + </options> + </param> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="vcf_samples" value="NA00001,NA00003"/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcfselectsamples-test1.vcf"/> + </test> + </tests> + <help> + +Allows to keep or remove samples from a VCF file. + +----- + +.. class:: infomark + + +**Example**: + +Selecting *NA00001* and *NA00003* from the following VCF line:: + + #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:.,. + +will, obviously, remove *NA00002*:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 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 2/2:35:4:.,. + +---- + +Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). +</help> + <expand macro="citations" /> +</tool> |