view taxon_set.xml @ 0:e3f1c47246fd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27

<tool id="checkm_taxon_set" name="CheckM taxon_set" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Generate taxonomic-specific marker set
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
checkm taxon_set
    '$rank_taxon.rank'
    '$rank_taxon.taxon.fields.value'
    '$marker'
    ]]></command>
    <inputs>
        <expand macro="rank_taxon"/>
    </inputs>
    <outputs>
        <expand macro="marker_output" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="rank_taxon">
                <param name="rank" value="life"/>
                <param name="taxon" value="Prokaryote"/>
            </conditional>
            <output name="marker" ftype="tabular">
                <assert_contents>
                    <has_text text="[Taxon Marker File]"/>
                    <has_text text="Prokaryote"/>
                    <has_text text="PF00318.15"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This command generates taxonomic-specific marker set
    ]]></help>
    <expand macro="citations"/>
</tool>