<tool id="LimmaAnalyse" name="Limma analysis" version="1.0.0">

    <description>Performs gene expression analysis thanks to limma</description>

    <requirements>
        <requirement type="package">bioconductor-biobase</requirement>
        <requirement type="package">bioconductor-geoquery</requirement>
        <requirement type="package">bioconductor-geometadb</requirement>
        <requirement type="package">bioconductor-limma</requirement>
        <requirement type="package">bioconductor-affy</requirement>
        <requirement type="package">r-jsonlite</requirement>
        <requirement type="package">r-dplyr</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__}/Analyse.R
            --rdatainput ${rdataset}
            --conditions ${conditions}
            --selectcondition1 "${selectCondition1}"
            --selectcondition2 "${selectCondition2}"
            --nbresult ${nbresult}
            --rdataoutput ${result_export_eset}
            --htmloutput $result_html 
            --htmloutputpath $result_html.files_path
            --tabularoutput $result_tabular
            --htmltemplate ${__tool_directory__}/Analyse_tpl.html
            --tooldirectory ${__tool_directory__}
        ]]>
    </command>

    <inputs>
        <param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
        <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
        <param name="selectCondition1" type="select" label="condition 1">
            <options from_dataset="conditions">
                <column name="name" index="1"/>
                <column name="value" index="1"/>
                <filter type="unique_value" column="1"/>
            </options>
        </param>
        <param name="selectCondition2" type="select" label="condition 2">
            <options from_dataset="conditions">
                <column name="name" index="1"/>
                <column name="value" index="1"/>
                <filter type="unique_value" column="1"/>
            </options>
        </param>	
        <param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
    </inputs>

    <outputs>
        <data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
        <data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
        <data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
    </outputs>

    <tests>
        <test>
            <param name="rdataset" value="GSE3524_data.rdata"/>
            <param name="conditions" value="conditions.cond"/>
            <param name="selectCondition1" value="series of 16 tumors"/>
            <param name="selectCondition2" value="series of 4 normals"/>
            <param name="nbresult" value="10"/>
            <output name="result_tabular" file="GSE3524_analysis.tabular" ftype="tabular"/>
        </test>
    </tests>

    <help>
<![CDATA[ 
**What it does**
		
The Limma analysis tool performs single analysis either of data previously retrieved from GEO database or normalized affymetrix .CEL files data. 
Given a .cond file, it runs a standard limma differential expression analysis. 

**Example** of .cond file      	

The .cond file should look like this 
::


 GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
 GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
 GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors
 GSM80476	series of 4 normals	GSM80476 OSCE-2N Series of 4 Normals
 GSM80477	series of 4 normals	GSM80477 OSCE-9N Series of 4 Normals
	
		
**Results**
		
- Boxplots, p-value histograms and a volcano plot 
- Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
- Rdata object to perform further meta-analysis. 
]]>
    </help>

</tool>