view tools/mothur/merge.taxsummary.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

<tool profile="16.07" id="mothur_merge_taxsummary" name="Merge.taxsummary" version="@WRAPPER_VERSION@.0">
    <description>Merge tax.summary files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        echo 'merge.taxsummary(
            input=${ str($input).replace(",","-") },
            output=$output
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur &&

        ## move output files to correct destination
        mv mothur.*.logfile "$logfile"
    ]]></command>
    <inputs>
        <param name="input" type="data" format="mothur.tax.summary" multiple="true" label="input - tax.summary files"/>
    </inputs>
    <outputs>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
        <data name="output" format="mothur.tax.summary" label="${tool.name} on ${on_string}: merged sff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="amazon.wang.knn.tax.summary,amazon.silva.wang.tax.summary"/>
            <output name="output" md5="6e1276cc740b03d5407a3707322e1ee3" ftype="mothur.tax.summary"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file.

.. _merge.taxsummary: http://www.mothur.org/wiki/Merge.taxsummary

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