| Previous changeset 1:829d46588cf5 (2015-11-11) Next changeset 3:6faa2c4c71d2 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml test-data/vcfannotate-test1.vcf vcfannotate.xml |
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removed:
tool_dependencies.xml |
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| diff -r 829d46588cf5 -r d64204113938 macros.xml --- a/macros.xml Wed Nov 11 12:57:42 2015 -0500 +++ b/macros.xml Thu Sep 15 16:07:40 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 829d46588cf5 -r d64204113938 test-data/vcfannotate-test1.vcf --- a/test-data/vcfannotate-test1.vcf Wed Nov 11 12:57:42 2015 -0500 +++ b/test-data/vcfannotate-test1.vcf Thu Sep 15 16:07:40 2016 -0400 |
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| @@ -28,5 +28,5 @@ 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;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 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 . +20 1235237 . T . 0 . . GT 0/0 0|0 ./. X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 |
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| diff -r 829d46588cf5 -r d64204113938 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:57:42 2015 -0500 +++ /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 829d46588cf5 -r d64204113938 vcfannotate.xml --- a/vcfannotate.xml Wed Nov 11 12:57:42 2015 -0500 +++ b/vcfannotate.xml Thu Sep 15 16:07:40 2016 -0400 |
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| @@ -1,51 +1,51 @@ -<tool id="vcfannotate" name="VCFannotate:" version="0.0.3"> - <description>Intersect VCF records with BED annotations</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input" type="data" label="Select VCF dataset"/> - <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/> - <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="bed_data" value="vcfannotate.bed" ftype="bed"/> - <param name="key_option" value="BED-features"/> - <param name="input" value="vcflib.vcf"/> - <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" /> - </test> - </tests> - <help> - -Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. - ------ - -.. class:: infomark - - -**Example**: - -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 appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen:: - - #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 - 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. - ----- - -Vcfannotate @IS_PART_OF_VCFLIB@ - </help> - <expand macro="citations" /> -</tool> +<tool id="vcfannotate" name="VCFannotate:" version="@WRAPPER_VERSION@.0"> + <description>Intersect VCF records with BED annotations</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input" type="data" label="Select VCF dataset"/> + <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/> + <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="bed_data" value="vcfannotate.bed" ftype="bed"/> + <param name="key_option" value="BED-features"/> + <param name="input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" /> + </test> + </tests> + <help> + +Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. + +----- + +.. class:: infomark + + +**Example**: + +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 appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 + 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. + +---- + +Vcfannotate @IS_PART_OF_VCFLIB@ + </help> + <expand macro="citations" /> +</tool> |