comparison bcftools_plugin_color_chrs.xml @ 8:47ee1925fe9e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

8:47ee1925fe9e

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1">
    <description>plugin Color shared chromosomal segments, requires phased GTs</description>
    <macros>
        <token name="@EXECUTABLE@">color-chrs</token>
        <token name="@PLUGIN_ID@">color_chrs</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@

bcftools plugin @EXECUTABLE@

## VCF input section
#set $section = $sec_restrict
@REGIONS@
@TARGETS@
@INCLUDE@
@EXCLUDE@

@THREADS@

## Primary Input/Outputs
@INPUT_FILE@

## Plugin options
#if $sample_relation.sample_rel_sel == 'trio':
-- --trio '${sample_relation.mother},${sample_relation.father},${sample_relation.child}'
#else:
-- --unrelated '${sample_relation.sample_a},${sample_relation.sample_b}'
#end if
-p output_tmp
&& color-chrs.pl output_tmp.dat -p output_tmp
&& mv output_tmp.dat '$output_data'
&& mv output_tmp.svg '$output_svg'
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <conditional name="sample_relation"> 
            <param name="sample_rel_sel" type="select" label="Sample relationship">
                <option value="trio">trio - mother,father,child</option>
                <option value="unrelated">unrelated sample pair</option>
            </param>
            <when value="trio">
               <param name="mother" type="text" value="" label="name of mother"/>
               <param name="father" type="text" value="" label="name of father"/>
               <param name="child" type="text" value="" label="name of child"/>
            </when>
            <when value="unrelated">
               <param name="sample_a" type="text" value="" label="name of sample A"/>
               <param name="sample_b" type="text" value="" label="name of sample B"/>
            </when>
        </conditional>
        <section name="sec_restrict" expanded="false" title="Restrict analysis to">
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
            <expand macro="macro_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
        </section>
    </inputs>
    <outputs>
        <data name="output_data" format="tabular" />
        <data name="output_svg" format="svg" />
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input_file" ftype="vcf" value="stats.a.vcf" />
            <conditional name="sample_relation">
                <param name="sample_rel_sel" value="trio" />
                <param name="mother" value="A" />
                <param name="father" value="C" />
                <param name="child" value="B" />
            </conditional>
            <output name="output_data" ftype="tabular" file="color_chrs.dat" />
        </test>
        <test expect_num_outputs="2">
            <param name="input_file" ftype="vcf" value="stats.a.vcf" />
            <conditional name="sample_relation">
                <param name="sample_rel_sel" value="unrelated" />
                <param name="sample_a" value="A" />
                <param name="sample_b" value="B" />
            </conditional>
            <output name="output_data" ftype="tabular" file="color_chrs_unrelated.dat" />
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@ plugin
=====================================

@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

]]>
</help>
    <expand macro="citations" />
</tool>