<tool id="humann2_merge_abundance_tables" name="Merge HUMAnN2 gene and pathway abundance tables" version="0.1.0">
    <description></description>

    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>
        <requirement type="package" version="2.0">metaphlan2</requirement>
        <requirement type="package" version="0.6.13">diamond</requirement>
        <requirement type="package" version="2.0">humann2</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
    </stdio>

    <version_command>
<![CDATA[
    humann2_merge_abundance_tables --version
]]>
    </version_command>

    <command><![CDATA[
        humann2_merge_abundance_tables
            --input-genes $input_gene
            --input-pathways $input_pathway
            --gene-mapping $gene_mapping
            --pathway-mapping $pathway-mapping
            $remove_taxonomy
                                  
            -o $output_table
    ]]></command>

    <inputs>
        <param name="input_gene" type="data" format="tsv" label="Gene family or EC 
            abundance file" help="(--input-genes)"/>
        <param name="input_pathway" type="data" format="tsv" label="Pathway 
            abundance file" help="(--input-pathways)"/>
        <param name="gene_mapping" type="data" format="tsv" label="Gene family 
            to reaction mapping file" help="(--gene-mapping)"/>
        <param name="pathway_mapping" type="data" format="tsv" label="Reaction to 
            pathway mapping file" help="(--pathway-mapping)"/>
        <param name='remove_taxonomy' type='boolean' checked="false" 
            truevalue='--remove-taxonomy' falsevalue='' 
            label="Remove the taxonomy from the output file?" 
            help="(--remove-taxonomy)"/>
        
    </inputs>

    <outputs>
        <data format="tsv" name="output_table" label="Merged table for 
            ${on_string} (HUMAnN2)" />
    </outputs>

    <tests>
    </tests>

    <help><![CDATA[
        **What it does**

        This tool merge gene and pathway abundance tables.

        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.

    ]]></help>

    <citations>
    </citations>
</tool>