<tool profile="16.07" id="mothur_parse_list" name="Parse.list" version="@WRAPPER_VERSION@.0">
    <description>Generate a List file for each group</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 '$otu' otu.dat &&
ln -s '$group' group.dat &&
ln -s '$count' count.dat &&

echo 'parse.list(
    list=otu.dat,
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $count:
        count=count.dat,
    #end if
    group=group.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
        <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
            <expand macro="labeloptions"/>
        </param>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.list"/>
            <param name="group" value="amazon.groups"/>
            <output_collection name="listfiles" count="72">
                <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="otu" value="amazon.an.list"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="label" value="0.03,0.05"/>
            <output_collection name="listfiles" count="4"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.

.. _list: https://www.mothur.org/wiki/List_file
.. _group: https://www.mothur.org/wiki/Group_file
.. _parse.list: https://www.mothur.org/wiki/Parse.list

v.1.19.0: Updated to mothur 1.33, added count parameter

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