view tools/mothur/shhh.seqs.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

<tool profile="16.07" id="mothur_shhh_seqs" name="Shhh.seqs" version="@WRAPPER_VERSION@.0">
    <description>Denoise program (Quince SeqNoise)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        echo 'shhh.seqs(
            fasta=$fasta,
            name=$name,
            #if $group:
                group=$group,
            #end if
            sigma=$sigma,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur &&

        ## move output files to correct destination
        prefix="$fasta" &&
        mv mothur.*.logfile "$logfile" &&
        mv \${prefix%.dat}*.shhh_seqs.fasta "$shhh_fasta" &&
        mv \${prefix%.dat}*.shhh_seqs.names "$shhh_names" &&
        mv \${prefix%.dat}*.shhh_seqs.map "$shhh_map"
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
        <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
        <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/>
    </inputs>
    <outputs>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
        <data name="shhh_fasta" format_source="fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
        <data name="shhh_names" format="mothur.names" label="${tool.name} on ${on_string}: shhh.names"/>
        <data name="shhh_map" format="txt" label="${tool.name} on ${on_string}: shhh.map"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/>
            <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/>
            <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/>
            <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.

.. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs

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