Mercurial > repos > iuc > bcftools_gtcheck
diff bcftools_gtcheck.xml @ 16:a29a2f40b665 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
---|---|
date | Tue, 20 Sep 2022 13:09:16 +0000 |
parents | 64778f8899cc |
children | 91c1e57d5c7f |
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--- a/bcftools_gtcheck.xml Sat Jul 23 13:37:10 2022 +0000 +++ b/bcftools_gtcheck.xml Tue Sep 20 13:09:16 2022 +0000 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Check sample identity</description> <macros> <token name="@EXECUTABLE@">gtcheck</token> @@ -47,10 +47,6 @@ ${section.all_sites} -#if $section.GTs_only: - --GTs-only '${section.GTs_only}' -#end if - ${section.homs_only} #if $section.plot: @@ -85,7 +81,6 @@ <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/> <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" /> - <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using <int> for unseen genotypes" /> <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" /> <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" /> <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" /> @@ -98,10 +93,9 @@ <tests> <test> <param name="input_file" ftype="vcf" value="view.vcf" /> - <param name="GTs_only" value="99" /> <output name="output_file"> <assert_contents> - <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/> + <has_text_matching expression="DC\tNA00002\tNA00001\t6"/> </assert_contents> </output> </test>