<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="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&

echo 'shhh.seqs(
    fasta=fasta.dat,
    name=name.dat,
    #if $group:
        group=group.dat,
    #end if
    sigma=$sigma,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></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"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
        <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/>
        <data name="shhh_map" format="txt" from_work_dir="fasta*.shhh_seqs.map" label="${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"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

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: https://www.mothur.org/wiki/Shhh.seqs

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pone.0027310</citation>
        <citation type="doi">10.1186/1471-2105-12-38</citation>
    </expand>
</tool>