comparison bcftools_plugin_setgt.xml @ 16:40daf124be88 draft

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

15:2c4941386820

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
    <description>plugin Sets genotypes</description>
    <macros>
        <token name="@EXECUTABLE@">setGT</token>
        <token name="@PLUGIN_ID@">setgt</token>
        <import>macros.xml</import>

@INPUT_FILE@

## Plugin section
#set $section = $sec_plugin
--
-t '$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">
            <expand macro="macro_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>

            <param name="target_gt" type="select" label="Target genotypes to change">
                <option value="./.">./. completely missing (. or ./., depending on ploidy)</option>
                <option value="./x">./x partially missing (./0 or .|1)</option>
                <option value=".">. partially or completely missing</option>
                <option value="a">a all genotypes</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="M">M major allele</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>
	</section>
        <expand macro="macro_select_output_type" />

16:40daf124be88

<?xml version='1.0' encoding='utf-8'?>
<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>
        <token name="@PLUGIN_ID@">setgt</token>
        <import>macros.xml</import>

@INPUT_FILE@

## Plugin section
#set $section = $sec_plugin
--
--target-gt '$section.target_gt'
--new-gt '$section.new_gt'
> '$output_file'
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" title="Restrict to">
            <expand macro="macro_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>

            <param name="target_gt" type="select" label="Target genotypes to change">
                <option value="./.">./. completely missing (. or ./., depending on ploidy)</option>
                <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 (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>
	</section>
        <expand macro="macro_select_output_type" />