<tool id="metaMA" name="Microarray data meta-analysis" version="1.0.0">

    <description>Performs meta-analysis thanks to metaMA.</description>

    <requirements>
        <requirement type="package">bioconductor-affy</requirement>
        <requirement type="package">bioconductor-annaffy</requirement>
        <requirement type="package">bioconductor-geoquery</requirement>
        <requirement type="package">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package">r-venndiagram</requirement>
        <requirement type="package">r-metama</requirement>
        <requirement type="package">r-optparse</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
        <regex match="Warning" source="both" level="warning"/>
    </stdio>

    <command>
        <![CDATA[ 
        Rscript 
        ${__tool_directory__}/MetaMA.R
            --input $input
            --species $species
            --htmloutput $result_html 
            --htmloutputpath $result_html.extra_files_path
            --htmltemplate ${__tool_directory__}/MetaMa_tpl.html
        ]]>
	</command>

    <inputs>
        <param format="rdata" name="input" multiple="true" type="data" optional="false" label="rdata files" help="rdata files containing the results of the analysis to be used in the meta-analysis"/>
        <param name="species" type="select" optionnal="false" label="species" help="species for annotation">
            <option value="org.Bt.eg.db">Bovine</option>
            <option value="org.Cf.eg.db">Canine</option>
            <option value="org.Gg.eg.db">Chicken</option>
            <option value="org.Dm.eg.db">Fly</option>
            <option value="org.Hs.eg.db">Human</option>
            <option value="org.Mm.eg.db">Mouse</option>
            <option value="org.Ss.eg.db">Pig</option>
            <option value="org.Rn.eg.db">Rat</option>
            <option value="org.Ce.eg.db">Worm</option>
            <option value="org.Dr.eg.db">Zebrafish</option>
        </param>
    </inputs>

    <outputs>
        <data format="html" name="result_html" label="Meta-analysis results"/>
    </outputs>

    <help>
<![CDATA[ 
**What it does**
		
Given several Rdata object this tool run a meta-analysis using the metaMA R package.
		
**Results**
		
- Venn Diagram summarizing the results of the meta-analysis
- A list of indicators to evaluate the quality of the performance of the meta-analysis
		
	- DE : Number of differentially expressed genes 
	- IDD (Integration Driven discoveries) : number of genes that are declared differentially expressed in the meta-analysis that were not identified in any of the single studies alone
	- Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis 
	- DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
	- IRR (Integration-driven Revision) : corresponding proportion of Loss
		
- Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
]]>
    </help>

</tool>