| Previous changeset 0:f0dae4ac267e (2015-03-19) Next changeset 2:690b1d846263 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml test-data/vcfbreakcreatemulti-test1.vcf vcfbreakcreatemulti.xml |
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removed:
tool_dependencies.xml |
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| diff -r f0dae4ac267e -r 3aa04b92957f macros.xml --- a/macros.xml Thu Mar 19 12:43:19 2015 -0400 +++ b/macros.xml Thu Sep 15 16:04:07 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 f0dae4ac267e -r 3aa04b92957f test-data/vcfbreakcreatemulti-test1.vcf --- a/test-data/vcfbreakcreatemulti-test1.vcf Thu Mar 19 12:43:19 2015 -0400 +++ b/test-data/vcfbreakcreatemulti-test1.vcf Thu Sep 15 16:04:07 2016 -0400 |
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| @@ -24,11 +24,11 @@ 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;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;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 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ ./1:21:6:23,27 ./1:2:0:18,2 ./.:35:4:.,. -20 1110696 rs6040355 A T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ ./1:21:6:23,27 ./1:2:0:18,2 1/1:35:4:.,. +20 1110696 rs6040355 A G 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|.:21:6:23,27 .|1:2:0:18,2 ./.:35:4:.,. +20 1110696 rs6040355 A T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ .|1:21:6:23,27 1|.:2:0:18,2 1/1:35:4:.,. 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 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 ./0:17:2 1/1:40:3 20 1234567 microsat1 G GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP ./0:.:4 0/1:17:2 ./.:40:3 -20 1235237 . T . 0 . . GT 0/0 0|0 . -X 10 rsTest AC A 10 PASS . GT 0 0/1 ./0 -X 10 rsTest AC ATG 10 PASS . GT 0 ./0 0/1 +20 1235237 . T . 0 . . GT 0/0 0|0 ./. +X 10 rsTest AC A 10 PASS . GT 0 0/1 0|. +X 10 rsTest AC ATG 10 PASS . GT 0 ./0 0|1 |
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| diff -r f0dae4ac267e -r 3aa04b92957f tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 19 12:43:19 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 f0dae4ac267e -r 3aa04b92957f vcfbreakcreatemulti.xml --- a/vcfbreakcreatemulti.xml Thu Mar 19 12:43:19 2015 -0400 +++ b/vcfbreakcreatemulti.xml Thu Sep 15 16:04:07 2016 -0400 |
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| @@ -1,53 +1,48 @@ -<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3"> - <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command> - - #if str($break_or_create) == "break": - vcfbreakmulti "${input1}" > "${out_file1}" - #elif str($break_or_create) == "create": - vcfcreatemulti "${input1}" > "${out_file1}" - #end if - -</command> - - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> - <param name="break_or_create" type="select" display="radio" label="Break or Create?"> - <option value="break">Break</option> - <option value="create">Create</option> - </param> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="break_or_create" value="break"/> - <param name="input1" value="vcflib.vcf"/> - <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> - </test> - <test> - <param name="break_or_create" value="create"/> - <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> - <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> - </test> - </tests> - <help> - -This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): - - - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. - - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. - ----- - -This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). - -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="@WRAPPER_VERSION@.0"> + <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command> + #if str($break_or_create) == "break": + vcfbreakmulti "${input1}" > "${out_file1}" + #elif str($break_or_create) == "create": + vcfcreatemulti "${input1}" > "${out_file1}" + #end if + </command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> + <param name="break_or_create" type="select" display="radio" label="Break or Create?"> + <option value="break">Break</option> + <option value="create">Create</option> + </param> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="break_or_create" value="break"/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> + </test> + <test> + <param name="break_or_create" value="create"/> + <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> + <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> + </test> + </tests> + <help> +This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): + + - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. + - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. + +---- + +This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + </help> + <expand macro="citations" /> +</tool> |