<tool profile="16.07" id="mothur_make_files" name="Make.group" version="@WRAPPER_VERSION@.0">
    <description>Make a group file</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 "$fasta" fasta.dat &&
        #for $i in $inputs:
            ln -s "$i.fasta" fasta${inputs.index($i)}.dat &&
        #end for

        echo 'make.group(
            fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
            groups=${group}#for $i in $inputs#-${i.group}#end for#
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
        <param name="group" type="text" label="group - Group name"/>
        <repeat name="inputs" title="Additional">
            <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
            <param name="group" type="text" label="group - Group name"/>
        </repeat>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="output" format="mothur.groups" from_work_dir="fasta*groups" label="${tool.name} on ${on_string}: group"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <param name="group" value="testgroup"/>
            <repeat name="inputs">
                <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
                <param name="group" value="testgroup2"/>
            </repeat>
            <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.

.. _group: http://www.mothur.org/wiki/Group_file
.. _make.group: http://www.mothur.org/wiki/Make.group

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