<tool profile="16.07" id="mothur_unique_seqs" name="Unique.seqs" version="@WRAPPER_VERSION@.0">
    <description>Return unique 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 '$names' names.dat &&
ln -s '$fasta' fasta.dat &&

echo 'unique.seqs(
    #if $names.is_of_type('mothur.names'):
        name=names.dat,
    #elif $names.is_of_type('mothur.count_table'):
        count=names.dat,
    #end if
    fasta=fasta.dat,
    format=$format
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
        <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/>
        <param name="format" type="select" label="output format">
            <option value="count" selected="true"> Count table </option>
            <option value="name"> Name file </option>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/>
        <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names">
            <filter> format == "name" </filter>
        </data>
        <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table">
            <filter> format == "count" </filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test with names file -->
            <param name="fasta" value="amazon.fasta"/>
            <param name="names" value="amazon1.names" ftype="mothur.names"/>
            <param name="format" value="name"/>
            <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
            <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with count file -->
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="names" value="amazon.count_table" ftype="mothur.count_table"/>
            <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
            <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test wth fasta only -->
            <param name="fasta" value="amazon.fasta"/>
            <param name="format" value="name"/>
            <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/>
            <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence.

.. _name: https://www.mothur.org/wiki/Name_file
.. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs

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