<tool profile="16.07" id="mothur_mimarks_attributes" name="Mimarks.attributes" version="@WRAPPER_VERSION@.0">
    <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</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 '$biosample_in' biosample_in.dat &&

echo 'mimarks.attributes(
    xml=biosample_in.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
        <!-- TODO: add package type options (currently none described in documentation apart from default)
        <param name="package" type="select" label="package - select the mimarks package you would like to use">
            <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
        </param>-->
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
    </outputs>
    <tests>
        <test>
            <param name="biosample_in" value="biosample.xml" ftype="xml"/>
            <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The mimarks.attributes_ command reads `BioSample Attributes`_ xml and generates source for get.mimarkspackage_ command.

.. _mimarks.attributes: https://www.mothur.org/w/index.php?search=mimarks.attributes
.. _BioSample Attributes: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
.. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage

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