<tool profile="16.07" id="mothur_summary_qual" name="Summary.qual" version="@WRAPPER_VERSION@.0">
    <description>Summarize the quality scores</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 '$qfile' qfile.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&

echo 'summary.qual(
    qfile=qfile.dat
    #if $name:
        ,name=name.dat
    #end if
    #if $count:
        ,count=count.dat
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/>
    </outputs>
    <tests>
        <test>
            <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
            <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.

.. _summary.qual: https://www.mothur.org/wiki/Summary.qual

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