annotate humann2_merge_abundance_tables.xml @ 0:3d6f37e7e3a8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

<tool id="humann2_merge_abundance_tables" name="Merge" version="0.6.1">
    <description> HUMAnN2 generated gene and pathway abundance tables</description>

    <macros>
        <import>humann2_macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="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

            #if $gene_mapping_selection.gene_mapping_selection_test == "true":
                --gene-mapping $gene_mapping
            #end if 

            #if $pathway_mapping_selection.pathway_mapping_selection_test == "true":
                --pathway-mapping $pathway-mapping
            #end if 

            $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)"/>

        <conditional name="gene_mapping_selection">
            <param name='gene_mapping_selection_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a gene mapping file?" help=""/>
                <when value="true">
                    <param name="gene_mapping" type="data" format="tsv" label="Gene family to reaction mapping file" help="(--gene-mapping)"/>
                </when>
                <when value="false">
                </when>
        </conditional>
        <conditional name="pathway_mapping_selection">
            <param name='pathway_mapping_selection_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a pathway mapping file?" help=""/>
                <when value="true">
                    <param name="pathway_mapping" type="data" format="tsv" label="Reaction to pathway mapping file" help="(--pathway-mapping)"/>
                </when>
                <when value="false">
                </when>
        </conditional>

        <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="${tool.name} on ${on_string}: Merged table" />
    </outputs>

    <tests>
        <test>
            <param name="input_gene" value="expected_gene_family_abundance.tsv"/>
            <param name="input_pathway" value="expected_pathway_abundance.tsv"/>
            <param name="gene_mapping_selection_test" value="false"/>
            <param name="pathway_mapping_selection" value="false"/>
            <param name="remove_taxonomy" value="false"/>
            <output name="output_table" file="merged_gene_families_pathways_abundances.tsv" /> 
        </test>
    </tests>

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

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>`_.

The currest tool merge a table containing gene family abundances with a table containing pathway abundances, given a gene to pathway mapping (default or custom one).

    ]]></help>

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