<tool profile="16.07" id="mothur_cluster_classic" name="Cluster.classic" version="@WRAPPER_VERSION@.0">
    <description>Assign sequences to OTUs (Dotur implementation)</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 "$dist" dist.dat &&
        ln -s "$name" name.dat &&
        ln -s "$count" count.dat &&

        echo 'cluster.classic(
            phylip=dist.dat,
            #if $name:
                name=name.dat,
            #end if
            #if $count:
                count=count.dat,
            #end if
            method=$method,
            #if $cutoff:
                cutoff=$cutoff,
            #end if
            hard=$hard,
            precision=$precision,
            sim=$sim
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <param name="method" type="select" label="method - Select a Clustering Method" help="">
            <option value="furthest">Furthest neighbor</option>
            <option value="nearest">Nearest neighbor</option>
            <option value="average" selected="true">Average neighbor</option>
            <option value="weighted">Weighted</option>
        </param>
        <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
        <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
        <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
            <option value="10">.1</option>
            <option value="100" selected="true">.01</option>
            <option value="1000">.001</option>
            <option value="10000">.0001</option>
            <option value="100000">.00001</option>
            <option value="1000000">.000001</option>
        </param>
        <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
        <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
        <data name="otulist" format="mothur.list" from_work_dir="dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
    </outputs>
    <tests>
        <test><!-- test with phylip and default params-->
            <param name="dist" value="env.dist"/>
            <output name="rabund" md5="b7f4b5ee46b2c4f5221d487e24dca9db" ftype="mothur.rabund"/>
            <output name="sabund" md5="ac2df77e39a106fa65fae3d2132bc4ea" ftype="mothur.sabund"/>
            <output name="otulist" ftype="mothur.list">
                <assert_contents>
                    <has_text text="group"/>
                    <has_text text="unique"/>
                    <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).

.. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic

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