<tool profile="16.07" id="mothur_get_mimarkspackage" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
    <description>creates a mimarks package form with your groups</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 '$input.infile' input.infile.dat &&

echo 'get.mimarkspackage(
    #if $input.filetype == "group":
        group=input.infile.dat,
    #elif $input.filetype == "oligos":
        oligos=input.infile.dat,
    #end if
    package=$package,
    requiredonly=$requiredonly
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="filetype" type="select" label="input type">
                <option value="group">group file</option>
                <option value="oligos" selected="true">oligos file</option>
            </param>
            <when value="group">
                <param name="infile" type="data" format="mothur.groups" label="group file"/>
            </when>
            <when value="oligos">
                <param name="infile" type="data" format="mothur.oligos" label="oligos"/>
            </when>
        </conditional>
        <param name="package" type="select" label="package - select the mimarks package you would like to use">
            <option value="air">air</option>
            <option value="host_associated">host_associated</option>
            <option value="human_associated">human_associated</option>
            <option value="human_gut">human_gut</option>
            <option value="human_oral">human_oral</option>
            <option value="human_skin">human_skin</option>
            <option value="human_vaginal">human_vaginal</option>
            <option value="microbial">microbial</option>
            <option value="miscellaneous" selected="true">miscellaneous</option>
            <option value="plant_associated">plant_associated</option>
            <option value="sediment">sediment</option>
            <option value="soil">soil</option>
            <option value="wastewater">wastewater</option>
            <option value="waterc">waterc</option>
        </param>
        <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/>
    </outputs>
    <tests>
        <test><!-- test with group file -->
            <param name="filetype" value="group"/>
            <param name="infile" value="amazon.groups" ftype="mothur.groups"/>
            <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos -->
            <param name="filetype" value="oligos"/>
            <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
            <param name="package" value="human_associated"/>
            <param name="requiredonly" value="true"/>
            <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.mimarkspackage_ command creates a mimarks package form with your groups.

.. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage

    ]]></help>
    <citations>
        <citation type="doi">10.1128/AEM.01541-09</citation>
    </citations>
</tool>