<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>
        <expand macro="param-savelog"/>
    </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"/>
            <param name="savelog" value="true"/>
            <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"/>
            <param name="savelog" value="true"/>
            <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>
    <expand macro="citations"/>
</tool>