view metaquantome_stat.xml @ 4:80ce9ca55697 draft

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<tool id="metaquantome_stat" name="metaQuantome: stat" version="@VERSION@.0">
    <description>differential analysis of functional expression and taxonomic abundance</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @MAKE_SAMPS_TSV@
        metaquantome stat
        --samps samp_file.tab
        --mode '$mode'
        --ontology '$ontology'
        --file '$file'
        --parametric '$parametric'
        $paired
        --outfile='$outfile'
    ]]></command>
    <inputs>
        <expand macro="SAMPS"/>
        <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
                    help=""/>
        <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>
        <param name="ontology" type="select" label="Ontology">
            <option value="go">Gene Ontology (GO) terms</option>
            <option value="ec">Enzyme Commission (EC) numbers</option>
            <option value="cog">COG (column named 'cog')</option>
        </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"/>
        <expand macro="output_samples_choice"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
        <expand macro="output_samples"/>
    </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" />
            <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
            <param name="samps_src" value="build" />
            <repeat name="samps">
                <param name="group_name" value="s1"/>
                <param name="col_names" value="int1,int2,int3"/>
            </repeat>
            <repeat name="samps">
                <param name="group_name" value="s2"/>
                <param name="col_names" value="int4,int5,int6"/>
            </repeat>
        </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>