Mercurial > repos > iuc > bcftools_plugin_setgt
diff bcftools_plugin_setgt.xml @ 16:40daf124be88 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
---|---|
date | Tue, 20 Sep 2022 13:03:05 +0000 |
parents | 99238dfb46cb |
children | a1aad8b559c6 |
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--- a/bcftools_plugin_setgt.xml Sat Jul 23 13:48:25 2022 +0000 +++ b/bcftools_plugin_setgt.xml Tue Sep 20 13:03:05 2022 +0000 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>plugin Sets genotypes</description> <macros> <token name="@EXECUTABLE@">setGT</token> @@ -33,14 +33,14 @@ ## Plugin section #set $section = $sec_plugin -- --t '$section.target_gt' +--target-gt '$section.target_gt' --new-gt '$section.new_gt' > '$output_file' ]]> </command> <inputs> <expand macro="macro_input" /> - <section name="sec_restrict" expanded="false" title="Restrict to"> + <section name="sec_restrict" title="Restrict to"> <expand macro="macro_restrict" /> <expand macro="macro_restrict" type="target" label_type="Target" /> <expand macro="macro_include" /> @@ -52,11 +52,15 @@ <option value="./x">./x partially missing (./0 or .|1)</option> <option value=".">. partially or completely missing</option> <option value="a">a all genotypes</option> + <option value="b">b heterozygous genotypes failing two-tailed binomial test</option> + <option value="q">q select genotypes using -i/-e options</option> </param> <param name="new_gt" type="select" label="New genotypes to set"> <option value=".">. missing (. or ./., keeps ploidy)</option> - <option value="0">0 reference allele</option> + <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option> + <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option> <option value="M">M major allele</option> + <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option> <option value="p">p phased genotype</option> <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option> </param>