<tool profile="16.07" id="mothur_make_lefse" name="Make.lefse" version="@WRAPPER_VERSION@.0">
    <description>create a lefse formatted input file from mothur's output 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
        ln -s "$otu" otu.dat &&
        ln -s "$design" design.dat &&
        ln -s "$constaxonomy" constaxonomy.dat &&

        echo 'make.lefse(
            #if $otu.is_of_type("mothur.relabund"):
                relabund=otu.dat,
            #else
                shared=otu.dat,
            #end if
            #if $design:
                design=design.dat,
            #end if
            #if $constaxonomy:
                constaxonomy=constaxonomy.dat,
            #end if
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            scale=$scale
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
        <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
            <expand macro="labeloptions"/>
        </param>
        <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="constaxonomy - provide a constaxonomy file"/>
        <param name="design" type="data" format="tabular" optional="true" label="design - provide your design file"/>
        <param name="scale" type="select" multiple="false" label="scale - select what scale you would like to use to convert your shared file abundances to relative abundances" help="">
            <option value="totalgroup" selected="true">totalgroup</option>
            <option value="totalotu">totalotu</option>
            <option value="averagegroup">averagegroup</option>
            <option value="averageotu">averageotu</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="lefse_out" format="tabular" from_work_dir="otu*.lefse" label="${tool.name} on ${on_string}: lefse"/>
    </outputs>
    <tests>
        <test><!-- test with shared file and defaults -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with relabund file -->
            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
            <param name="design" value="toymothur.design2" ftype="tabular"/>
            <param name="label" value="0.18"/>
            <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.

.. _make.lefse: https://www.mothur.org/wiki/Make.lefse

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