<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="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @SHELL_OPTIONS@

        ## create symlinks to input datasets
        #for $i in $input:
            ln -s "$i" input${input.index($i)}.dat &&
        #end for

        echo 'merge.taxsummary(
            input=#for $i in $input#input${input.index($i)}.dat-#end for#,
            output=$output
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | sed 's/-,/,/g'
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="input" type="data" format="mothur.tax.summary" multiple="true" label="input - tax.summary files"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <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: https://www.mothur.org/wiki/Main_Page

**Command Documentation**

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

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

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