view humann2_unpack_pathways.xml @ 2:7f208f1eb64f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908"

<tool id="humann2_unpack_pathways" name="Unpack pathway abundances to show genes included" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann2_unpack_pathways
    --input-genes '$input_genes'
    --input-pathways '$input_pathways'
    #if $gene_mapping
        --gene-mapping '$gene_mapping'
    #end if
    #if $pathway_mapping
        --pathway-mapping '$pathway_mapping'
    #end if               
    $remove_taxonomy
    --output '$output'
    ]]></command>
    <inputs>
        <param name="input_genes" argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
        <param name="input_pathways" argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
        <param name="gene_mapping" argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
        <param name="pathway_mapping" argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
        <param name="remove_taxonomy" argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
    </inputs>
    <outputs>
        <data format="tsv" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_genes" value="demo_genefamilies.tsv"/>
            <param name="input_pathways" value="demo_pathabundance.tsv"/>
            <param name="remove_taxonomy" value=""/>
            <output name="output" md5="993534d3e8fea242066352a0e4d67c8a"/>
        </test>
        <test>
            <param name="input_genes" value="demo_genefamilies.tsv"/>
            <param name="input_pathways" value="demo_pathabundance.tsv"/>
            <param name="remove_taxonomy" value="--remove-taxonomy"/>
            <output name="output" md5="b145ce760ce656b9e3ddb00d3ff4cf46"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

This utility will unpack the pathways to show the genes for each. It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
    ]]></help>
    <expand macro="citations"/>
</tool>