view tools/mothur/get.mimarkspackage.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

<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="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        echo 'get.mimarkspackage(
            #if $input.filetype == "group":
                group=$input.infile,
            #elif $input.filetype == "oligos":
                oligos=$input.infile,
            #else:
                file=$input.infile,
            #end if
            package=$package,
            requiredonly=$requiredonly
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur &&

        ## move output files to correct destination
        prefix="$input.infile" &&
        mv \${prefix%.dat}*.tsv "$package_out" &&
        mv mothur.*.logfile "$logfile"
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="filetype" type="select" label="description">
                <option value="group">group file</option>
                <option value="oligos" selected="true">oligos file</option>
                <option value="file">other file (e.g. output from mimarks.attributes)</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>
            <when value="file">
                <param name="infile" type="data" format="txt" label="file"/>
            </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"/>
    </inputs>
    <outputs>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
        <data name="package_out" format="tabular" label="${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"/>
            <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"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with other file (output from mimarks.attributes)-->
            <param name="filetype" value="file"/>
            <param name="infile" value="biosample.source" ftype="txt"/>
            <output name="package_out" file="biosample.tsv" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

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

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

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