<tool profile="16.07" id="mothur_get_oturep" name="Get.oturep" version="@WRAPPER_VERSION@.0">
    <description>Generate a fasta with a representative sequence for each OTU</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        ## create symlinks to input datasets
        ln -s "$otu" otu.dat &&
        ln -s "$fasta" fasta.dat &&
        ln -s "$input.dist" input.dist.dat &&
        ln -s "$input.name" input.name.dat &&
        ln -s "$count" count.dat &&
        #if $pick.type == "yes":
            ln -s "$pick.group" pick.group.dat &&
        #end if

        echo 'get.oturep(
            list=otu.dat,
            #if $fasta:
                fasta=fasta.dat,
            #end if
            #if $input.source == "column":
                column=input.dist.dat,
                name=input.name.dat,
            #elif $input.source == "phylip":
                phylip=input.dist.dat,
                #if $input.name:
                    name=input.name.dat,
                #end if
            #end if
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            #if $pick.type == "yes":
                #if $pick.group:
                    group=pick.group.dat,
                #end if
                #if $pick.groups:
                    groups=${ str($pick.groups).replace(",","-") },
                #end if
            #end if
            #if $sorted:
                sorted=$sorted,
            #end if
            #if $count and not $input.name:
                count=count.dat,
            #end if
            method=$method,
            large=$large
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <conditional name="input">
            <param name="source" type="select" label="Distance Matrix Format">
                <option value="column">Pairwise Column Distance Matrix</option>
                <option value="phylip">Phylip Distance Matrix</option>
            </param>
            <when value="column">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
            </when>
            <when value="phylip">
                <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
                <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
            </when>
        </conditional>
        <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/>
        <conditional name="pick">
            <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="group" type="data" format="mothur.groups" label="group - Group file for the OTU List"/>
                <param name="groups" type="select"  multiple="true" label="groups - Group Selection (all used if none are selected)">
                    <options>
                        <filter type="data_meta" ref="group" key="groups"/>
                    </options>
                </param>
            </when>
        </conditional>
        <param name="label" type="select" multiple="true" label="label - OTU Labels">
            <expand macro="labeloptions"/>
        </param>
        <param name="sorted" type="select" label="sorted - Sort Sequences by">
            <option value="">Don't sort</option>
            <option value="name">Sequence Name</option>
            <option value="number">Bin Number</option>
            <option value="size">Bin Size</option>
            <option value="group">Group</option>
        </param>
        <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="Cannot supply both a names and count table. Will be ignored if you also supplied a name file. Generated by count.seqs"/>
        <param name="method" type="select" label="method - select the method of selecting the representative sequence" help="the distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the abundant sequence in the OTU as the representative. Default=distance">
            <option value="distance" selected="true">distance</option>
            <option value="abundance">abundance</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
            <filter>input['name'] or not count</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.names" format="mothur.names"/>
        </collection>
        <collection name="fasta_out" type="list" label="${tool.name} on ${on_string}: rep.fasta">
            <filter>fasta</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.fasta" format="fasta"/>
        </collection>
        <collection name="count_out" type="list" label="${tool.name} on ${on_string}: rep.count_table">
            <filter>count and not input['name']</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.count_table" format="mothur.count_table"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with phylip -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="source" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="name" value="amazon1.names" ftype="mothur.names"/>
            <output_collection name="names_out" count="36">
                <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with column and label select -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="source" value="column"/>
            <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
            <param name="name" value="amazon1.names" ftype="mothur.names"/>
            <param name="label" value="unique,0.05,0.27,0.45"/>
            <output_collection name="names_out" count="4">
                <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with fasta and sorting-->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="source" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="label" value="0.05,0.27"/>
            <param name="sorted" value="name"/>
            <output_collection name="names_out" count="2">
                <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
            </output_collection>
            <output_collection name="fasta_out" count="2">
                <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group file -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="source" value="column"/>
            <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
            <param name="name" value="amazon1.names" ftype="mothur.names"/>
            <param name="label" value="unique,0.05,0.27,0.45"/>
            <param name="type" value="yes"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="forest,pasture"/>
            <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/> <!-- should be ignored as we also supplied name file -->
            <output_collection name="names_out" count="8">
                <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with count table -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="source" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="label" value="unique,0.05,0.27"/>
            <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
            <output_collection name="count_out" count="3">
                <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@


**Command Documenation**

The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU.  The opposite of the bin.seqs command.

.. _get.oturep: http://www.mothur.org/wiki/Get.oturep

v1.23.0: Updated to Mothur 1.33, added count and method parameter
]]>
    </help>
    <expand macro="citations"/>
</tool>