annotate bcftools_plugin_fill_tags.xml @ 7:e493702b19eb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
    <description>plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi</description>
    <macros>
        <token name="@EXECUTABLE@">fill-tags</token>
        <token name="@PLUGIN_ID@">fill_tags</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
@INCLUDE@
@EXCLUDE@
@REGIONS@
@TARGETS@

@OUTPUT_TYPE@
@THREADS@

## Primary Input/Outputs
@INPUT_FILE@

#set $section = $sec_plugin
#if $section.tags:
-- --tags "${section.tags}"
@SAMPLES@
#end if
> '$output_file'
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <section name="sec_plugin" expanded="true" title="Plugin Options">
            <param name="tags" type="select" multiple="true" label="TAGs to set">
                <option value="AF">AF</option>
                <option value="AN">AN</option>
                <option value="AC">AC</option>
                <option value="AC_Hom">AC_Hom</option>
                <option value="AC_Het">AC_Het</option>
                <option value="AC_Hemi">AC_Hemi</option>
                <option value="HWE">HWE</option>
            </param>
            <expand macro="macro_samples" />
        </section>
        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="AN=0" />
                    <has_text text="AC=0" />
                    <has_text text="AC_Het=0" />
                    <has_text text="AC_Hom=0" />
                    <has_text text="AC_Hemi=0" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
            <param name="output_type" value="v" />
            <param name="tags" value="AC_Het,AC_Hom" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="AC_Het=0" />
                    <has_text text="AC_Hom=0" />
                    <not_has_text text="AC_Hemi=0" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@ plugin
=====================================

@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

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