<tool id="metaquantome_stat" name="metaQuantome: stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>differential analysis of functional expression and taxonomic abundance</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        metaquantome stat
        --samps '$samps'
        --mode '$mode_args.mode'
        #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
            --ontology='$mode_args.ontology_args.ontology'
        #end if
        --file '$file'
        --control_group '$control_group'
        --parametric '$parametric'
        $paired
        --outfile='$outfile'
    ]]></command>
    <inputs>
        <expand macro="SAMPS"/>
        <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
                    help=""/>
        <conditional name="mode_args">
            <param argument="--mode" type="select" label="Mode">
                <option value="f">Functional analysis</option>
                <option value="t">Taxonomic analysis</option>
                <option value="ft">Functional-taxonomic interaction analysis</option>
            </param>
            <when value="f">
                <expand macro="ONTOLOGY_ARGS"/>
            </when>
            <when value="t">
            </when>
            <when value="ft">
                <expand macro="ONTOLOGY_ARGS"/>
            </when>
        </conditional>
        <param argument="--control_group" type="text" label="Name of the control sample group of control (used as denominator for fold change evaluation).">
            <validator type="empty_field"/>
        </param>
        <param argument="--parametric" type="select" label="Statistical test to perform">
            <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
            <option value="True">standard t-test (parametric)</option>
        </param>
        <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
    </outputs>
    <tests>
      <test>
        <param name="file" value="ec_ttest.tab" ftype="tabular" />
        <param name="parametric" value="True" />
        <param name="ontology" value="ec" />
        <param name="mode" value="f" />
        <param name="samps" value="samples_basic.tab" ftype="tabular" />
        <param name="control_group" value="s2"/>
        <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
      </test>
    </tests>
    <help><![CDATA[
metaQuantome stat
===================

The *stat* module is the third step in the metaQuantome analysis workflow. The purpose
of the *stat* module is to perform differential expression analysis between 2 experimental
conditions. metaQuantome offers paired and unpaired tests,
as well as parametric and non-parametric options.

Questions, Comments, Problems, Kudos
--------------------------------------

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.

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