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view abundanceTable_to_biom/abundanceTable_to_biom.xml @ 6:80877c2fc880 draft default tip

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author czouaoui
date Tue, 20 Mar 2018 05:12:29 -0400
parents d2f523789a27
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<tool id="abundanceTable_to_biom" name="Converting abundance tables to Biom files (v1.0)" version="0.1.0">
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/abundanceTable_to_biom.py --file $input --out_name biom_result
    ]]></command>
    <inputs>
        <param type="data" name="input" format="csv" label="Abundance table"/>
    </inputs>
    <outputs>
        <data name= "output" format="biom1" label="${input.name} to Biom (v1.0)" from_work_dir="biom_result.biom"/>
    </outputs>
    <tests>
        <test>
            <param name="input" format="csv" value="merge_summary_reads.csv"/>
            <output name="output" format="biom1" file="biom_result.biom"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool is used to generate a Biom file (v1.0) from an abundance table. 
	The first column of the header is a taxonomy list (families). Next columns contain sample ids.
	The abundancy of reads is set inside the table. 
    ]]></help>
</tool>