| Previous changeset 0:6e0fc18309f4 (2015-03-19) Next changeset 2:5822b40f3037 (2020-01-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml test-data/vcfdistance-test1.vcf vcfdistance.xml |
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removed:
tool_dependencies.xml |
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| diff -r 6e0fc18309f4 -r 48e458c721b3 macros.xml --- a/macros.xml Thu Mar 19 14:26:53 2015 -0400 +++ b/macros.xml Thu Sep 15 16:05:01 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 6e0fc18309f4 -r 48e458c721b3 test-data/vcfdistance-test1.vcf --- a/test-data/vcfdistance-test1.vcf Thu Mar 19 14:26:53 2015 -0400 +++ b/test-data/vcfdistance-test1.vcf Thu Sep 15 16:05:01 2016 -0400 |
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| @@ -23,7 +23,10 @@ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 19 111 . A C 9.6 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 19 112 . A G 10 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 -20 17330 . T A 3 q10 AF=0.017;BasesToClosestVariant=1093366;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 14370 rs6054257 G A 29 PASS AF=0.5;BasesToClosestVariant=2960;DP=14;NS=3;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 AF=0.017;BasesToClosestVariant=2960;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;BasesToClosestVariant=119541;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;BasesToClosestVariant=4330;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;BasesToClosestVariant=670;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 +20 1235237 . T . 0 . BasesToClosestVariant=670 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 6e0fc18309f4 -r 48e458c721b3 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 19 14:26:53 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 6e0fc18309f4 -r 48e458c721b3 vcfdistance.xml --- a/vcfdistance.xml Thu Mar 19 14:26:53 2015 -0400 +++ b/vcfdistance.xml Thu Sep 15 16:05:01 2016 -0400 |
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| @@ -1,34 +1,34 @@ -<tool id="vcfdistance" name="VCFdistance:" version="0.0.3"> - <description>Calculate distance to the nearest variant</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>cat "${input1}" | vcfdistance > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input1" value="vcflib.vcf"/> - <output name="out_file1" file="vcfdistance-test1.vcf"/> - </test> - </tests> - <help> - -Adds a value to each VCF record indicating the distance to the nearest variant in the file. - -.. class:: infomark - -The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). - ----- - -Vcfdistance @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfdistance" name="VCFdistance:" version="@WRAPPER_VERSION@.0"> + <description>Calculate distance to the nearest variant</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>cat "${input1}" | vcfdistance > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcfdistance-test1.vcf"/> + </test> + </tests> + <help> + +Adds a value to each VCF record indicating the distance to the nearest variant in the file. + +.. class:: infomark + +The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). + +---- + +Vcfdistance @IS_PART_OF_VCFLIB@ +</help> + <expand macro="citations" /> +</tool> |