<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 $count:
        count=count.dat,
    #end if
    fasta=fasta.dat,
    list=otu.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
        <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
        <param argument="label" type="select" multiple="true" label="label - OTU Labels">
            <expand macro="labeloptions"/>
        </param>
        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table"
            help="Represents the number of duplicate sequences for a given representitive sequence"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="fastafiles" type="list" label="${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" ftype="fasta">
                    <assert_contents>
                        <expand macro="test-fasta-format"/>
                        <has_text text="U68589"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <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" ftype="fasta">
                    <assert_contents>
                        <expand macro="test-fasta-format"/>
                        <has_text text="U68589"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <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>