Mercurial > repos > devteam > vcfallelicprimitives
changeset 2:0a69cff7946e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfallelicprimitives commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:07:24 -0400 |
| parents | f49b23b41a12 |
| children | a8a4f94aa321 |
| files | macros.xml test-data/vcfallelicprimitives-test1.vcf tool_dependencies.xml vcfallelicprimitives.xml |
| diffstat | 4 files changed, 6 insertions(+), 11 deletions(-) [+] |
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--- a/macros.xml Wed Nov 11 12:57:29 2015 -0500 +++ b/macros.xml Thu Sep 15 16:07:24 2016 -0400 @@ -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">
--- a/test-data/vcfallelicprimitives-test1.vcf Wed Nov 11 12:57:29 2015 -0500 +++ b/test-data/vcfallelicprimitives-test1.vcf Thu Sep 15 16:07:24 2016 -0400 @@ -30,6 +30,6 @@ 20 1110696 . A G,T 67 PASS AF=0.333,0.667;LEN=1,1;TYPE=snp,snp;Split primitives GT 1|2 2|1 2|2 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 . G GA,GAC 50 PASS AC=3,1;LEN=1,2;TYPE=ins,ins;Split primitives GT 0|1 0|2 1|1 -20 1235237 . T . 0 . . GT 0/0 0|0 . +20 1235237 . T . 0 . . GT 0/0 0|0 ./. X 10 . AC ATC,A 10 PASS LEN=1,1;TYPE=ins,del;Split primitives GT 0 0|2 0|1 X 11 . C G 10 PASS LEN=1;TYPE=snp;Split primitives GT 0 0|0 0|1
--- a/tool_dependencies.xml Wed Nov 11 12:57:29 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>
--- a/vcfallelicprimitives.xml Wed Nov 11 12:57:29 2015 -0500 +++ b/vcfallelicprimitives.xml Thu Sep 15 16:07:24 2016 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.3"> +<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="@WRAPPER_VERSION@.0"> <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description> <macros> <import>macros.xml</import> @@ -10,7 +10,7 @@ cat "${input}" | vcfallelicprimitives ${m_option} -t "${t_option}" - -L "${max_length}" + -L "${max_length}" $keep_info $keep_geno > "${out_file1}" </command> @@ -18,7 +18,7 @@ <param format="vcf" name="input" type="data" label="Select VCF dataset"/> <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/> <param name="t_option" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/> - <param name="max_length" type="integer" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/> + <param name="max_length" type="integer" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/> <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False" label="Maintain site and allele-level annotations when decomposing" help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition. For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/>