<tool profile="16.07" id="mothur_lefse" name="Lefse" version="@WRAPPER_VERSION@.0">
    <description>description</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 '$otu' shared.dat &&
ln -s '$design' design.dat &&

echo 'lefse(
    shared=shared.dat,
    design=design.dat,
    #if $class:
        class=$class,
    #end if
    #if $sclass:
        subclass=$sclass,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $sets:
        sets=${ str($sets).replace(",","-") },
    #end if
    aalpha=$aalpha,
    walpha=$walpha,
    lda=$lda,
    iters=$iters,
    fboots=$fboots,
    strict=$strict,
    minc=$minc,
    wilc=$wilc,
    curv=$curv,
    norm=$norm
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <param name="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
        <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
            <expand macro="labeloptions"/>
        </param>
        <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
        <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
        <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
            help="The set names are separated by dashes. The defualt is all sets in designfile">
            <options>
                <filter type="data_meta" ref="design" key="sets"/>
            </options>
         </param>
         -->
        <param name="class" type="text" optional="true" value="" label="class -indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided first category is used"/>
        <param name="sclass" type="text" optional="true" value="" label="subclass - indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided second category is used"/>
        <param name="aalpha" type="float" value="0.05" label="aalpha - alpha value for the Krukal Wallis Anova test" help=""/>
        <param name="walpha" type="float" value="0.05" label="walpha - alpha value for the Wilcoxon test" help=""/>
        <param name="lda" type="float" value="2.0" label="lda - threshold on the absolute value of the logarithmic LDA score" help=""/>
        <param name="iters" type="integer" value="30" min="0" label="iters - number of bootstrap iteration for LDA" help=""/>
        <param name="fboots" type="float" value="0.67" label="fboots - set the subsampling fraction value for each bootstrap iteration" help=""/>
        <param name="strict" type="integer" value="0" min="0" max="2" label="strict - set the multiple testing correction options" help=" 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison"/>
        <param name="minc" type="integer" value="10" min="0" label="minc - minimum number of samples per subclass for performing wilcoxon test" help=""/>
        <param name="wilc" type="boolean" truevalue="T" falsevalue="F" checked="true" label="wilc - indicate whether to perform the Wilcoxon test" help=""/>
        <param name="curv" type="boolean" truevalue="T" falsevalue="F" checked="false" label="curv - whether perform the wilcoxon testing the Curtis's approach (beta)" help=""/>
        <param name="norm" type="boolean" truevalue="T" falsevalue="F" checked="true" label="norm - multiply relative abundances by 1000000" help="Recommended when very low values are present"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="shared.*lefse_summary" label="${tool.name} on ${on_string}: summary"/>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
            <param name="design" value="mouse.design"/>
            <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label and class select -->
            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
            <param name="design" value="mouse.design"/>
            <param name="label" value="1"/>
            <param name="class" value="dpw"/>
            <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with sets -->
            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
            <param name="design" value="mouse.design"/>
            <param name="sets" value="8,142"/>
            <param name="label" value="1"/>
            <param name="class" value="dpw"/>
            <output name="summary" md5="64ebfb48d8c3e0bcd993a7ea8aa60e62" ftype="tabular"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[
@MOTHUR_OVERVIEW@


**Command Documentation**


.. _lefse: https://www.mothur.org/wiki/Lefse
    ]]></help>
    <expand macro="citations"/>
</tool>