<tool profile="16.07" id="mothur_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0">
    <description>Summarize the quality of sequences</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 '$count' count.dat &&

echo 'summary.seqs(
    fasta=fasta.dat,
    #if $name:
        name=name.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
        <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
            <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test names input -->
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="name" value="amazon.names"/>
            <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test count input -->
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="count" value="amazon.count_table"/>
            <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.


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

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