diff bcftools_plugin_setgt.xml @ 16:40daf124be88 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

--- 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>