annotate format_metaphlan2_output.xml @ 3:2c87f56bd53a draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

<tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.2.0">
    <description>output to extract abundance at different taxonomic levels</description>
    <requirements>
    </requirements>
    <xrefs>
        <xref type="bio.tools">format_metaphlan2_output</xref>
    </xrefs>

    <stdio>
    </stdio>

    <version_command></version_command>

    <command><![CDATA[
        python '$__tool_directory__/format_metaphlan2_output.py'
            --metaphlan2_output '$input_file'
            --all_taxo_level_abundance_file '$all_taxo_level_abundance_file'
            --kingdom_abundance_file '$kingdom_abundance_file'
            --phylum_abundance_file '$phylum_abundance_file'
            --class_abundance_file '$class_abundance_file'
            --order_abundance_file '$order_abundance_file'
            --family_abundance_file '$family_abundance_file'
            --genus_abundance_file '$genus_abundance_file'
            --species_abundance_file '$species_abundance_file'
            --strains_abundance_file '$strains_abundance_file'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/>
    </inputs>
    <outputs>
        <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" />
        <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" />
        <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" />
        <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" />
        <data name="order_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Order abundances" />
        <data name="family_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Family abundances" />
        <data name="genus_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Genus abundances" />
        <data name="species_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Species abundances" />
        <data name="strains_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Stain abundances" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="metaphlan2_output.txt"/>
            <output name="all_taxo_level_abundance_file" file="all_taxo_level_abundance.txt"/>
            <output name="kingdom_abundance_file" file="kingdom_abundance.txt"/>
            <output name="phylum_abundance_file" file="phylum_abundance.txt"/>
            <output name="class_abundance_file" file="class_abundance.txt"/>
            <output name="order_abundance_file" file="order_abundance.txt"/>
            <output name="family_abundance_file" file="family_abundance.txt"/>
            <output name="genus_abundance_file" file="genus_abundance.txt"/>
            <output name="species_abundance_file" file="species_abundance.txt"/>
            <output name="strains_abundance_file" file="strains_abundance.txt"/>
        </test>
    </tests>

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

This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).

9 files are generated: one file per taxonomic levels with abundance for corresponding clades and one file combining all taxonomic levels and corresponding abundances.
    ]]></help>

    <citations>
    </citations>
</tool>