<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="biotools"/>
    <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
    precision=$precision,
    sim=$sim
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="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 argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <param argument="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 argument="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold"
            help="Ignore pairwise distances larger than this. Default for methods opti,agc,dgc is 0.03, default for the other methods is 0.15"/>
        <param argument="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 argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
        <expand macro="param-savelog"/>
    </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>
            <param name="savelog" value="true"/>
            <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">
        <citation type="doi">10.1128/AEM.02810-10</citation>
        <citation type="doi">10.1128/AEM.71.3.1501-1506.2005</citation>
    </expand>
</tool>