<tool profile="16.07" id="mothur_make_design" name="Make Design" version="@WRAPPER_VERSION@.0">
    <description>Assign groups to Sets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

#for $grouping in $groupings:
    #set grp_str = $grouping.groups.__str__
    #if grp_str:
        #for $grp in grp_str.split(','):
            echo -e "$grp\t$grouping.name" >> $design;
        #end for
    #end if
#end for
    ]]></command>
    <inputs>
        <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
        <repeat name="groupings" title="Grouping">
            <param name="name" type="text" label="Name for a new combined grouping"/>
            <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
                <options>
                    <filter type="data_meta" ref="source" key="groups"/>
                </options>
            </param>
        </repeat>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/>
    </outputs>
    <tests>
        <test>
            <param name="source" value="amazon.mothur.shared" ftype="mothur.shared"/>
            <repeat name="groupings">
                <param name="name" value="tardis"/>
                <param name="groups" value="forest,pasture"/>
            </repeat>
            <repeat name="groupings">
                <param name="name" value="dalek"/>
                <param name="groups" value="pasture"/>
            </repeat>
            <output name="design" file="toymothur.design" ftype="mothur.design"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.

.. _merge.groups: https://www.mothur.org/wiki/Merge.groups
.. _indicator: https://www.mothur.org/wiki/Indicator
.. _metastats: https://www.mothur.org/wiki/Metastats

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