<tool profile="16.07" id="mothur_pairwise_seqs" name="Pairwise.seqs" version="@WRAPPER_VERSION@.0">
    <description>calculate uncorrected pairwise distances between 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 &&

        echo 'pairwise.seqs(
            fasta=fasta.dat,
            align=$align,
            #if $calc:
                calc=$calc,
            #end if
            $countends
            #if float($cutoff) > 0.0:
                cutoff=$cutoff,
            #end if
            #if $scoring.setby == "user":
                match=$scoring.match,
                mismatch=$scoring.mismatch,
                gapopen=$scoring.gapopen,
                gapextend=$scoring.gapextend,
            #end if
            #if $output:
                output=$output,
            #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" label="fasta - Fasta"/>
        <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
            <option value="needleman" selected="true">needleman (default)</option>
            <option value="gotoh">gotoh</option>
            <option value="blast">blast</option>
        </param>
        <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
            <option value="" selected="true">use default</option>
            <option value="onegap">onegap - counts a string of gaps as a single gap</option>
            <option value="nogaps">nogaps - ignores gaps</option>
            <option value="eachgap">eachgap - penalize each gap</option>
        </param>
        <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/>
        <param name="cutoff" type="float" value="0.0" min="0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/>
        <conditional name="scoring">
            <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
                <option value="default" selected="true">Use default settings</option>
                <option value="user">Manually set scoring values</option>
            </param>
            <when value="default"/>
            <when value="user">
                <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
                <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
                <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
                <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
            </when>
        </conditional>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
            <option value="" selected="true">Column-Formatted Matrix (Default)</option>
            <option value="lt">Phylip formatted Lower Triangle Matrix</option>
            <option value="square">Phylip formatted Square Matrix</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
            <change_format>
                <when input="output" value="lt" format="mothur.lower.dist"/>
                <when input="output" value="square" format="mothur.square.dist"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="align" value="needleman"/>
            <param name="calc" value=""/>
            <param name="countends" value=""/>
            <param name="cutoff" value="0.0"/>
            <param name="setby" value="default"/>
            <param name="output" value=""/>
            <expand macro="logfile-test"/>
            <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/>
        </test>
        <test>
            <param name="fasta" value="amazon.unique.fasta"/>
            <param name="align" value="gotoh"/>
            <param name="calc" value="onegap"/>
            <param name="countends" value="countends=false,"/>
            <param name="cutoff" value="0.01"/>
            <param name="setby" value="user"/>
                <param name="match" value="2"/>
                <param name="mismatch" value="-1"/>
                <param name="gapopen" value="-2"/>
                <param name="gapextend" value="-1"/>
            <param name="output" value="lt"/>
            <expand macro="logfile-test"/>
            <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

.. _Mothur: https://www.mothur.org/wiki/Main_Page

**Command Documentation**

The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or  phylip-formatted_distance_matrix_.

.. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs

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