<tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
    <description>Order Sequences by OTU</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 "$name" name.dat &&
        ln -s "$group" group.dat &&
        ln -s "$fasta" fasta.dat &&
        ln -s "$otu" otu.dat &&
        ln -s "$count" count.dat &&

        echo 'bin.seqs(
            #if $name:
                name=name.dat,
            #end if
            #if $group:
                group=group.dat,
            #end if
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            #if $count:
                count=count.dat,
            #end if
            fasta=fasta.dat,
            list=otu.dat
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="amazon.an.list"/>
            <param name="fasta" value="amazon.fasta"/>
            <output_collection name="fastafiles" count="36">
                <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group and name file and label select -->
            <param name="otu" value="amazon.an.list"/>
            <param name="fasta" value="amazon.fasta"/>
            <param name="name" value="amazon.names"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="label" value="0.03,0.05,0.22"/>
            <output_collection name="fastafiles" count="3">
                <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.

.. _list_file: https://www.mothur.org/wiki/List_file
.. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
]]>
    </help>
    <expand macro="citations"/>
</tool>