<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0">

    <description>Performs meta-analysis thanks to metaRNAseq</description>

    <requirements>
        <requirement type="package">bioconductor-affy</requirement>
        <requirement type="package">bioconductor-annaffy</requirement>
        <requirement type="package">bioconductor-geoquery</requirement>
        <requirement type="package">r-venndiagram</requirement>
        <requirement type="package">r-jsonlite</requirement> 
        <requirement type="package">r-metarnaseq</requirement>
        <requirement type="package">r-optparse</requirement>
        <requirement type="package" version="1.3.3">r-upsetr</requirement>
    </requirements>	

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

    <command>

<![CDATA[   
        Rscript 
        ${__tool_directory__}/MetaRNASeq.R 
            --input "#for $s in $studies: 
                        ${s.input};
                     #end for
"
            --inputName "#for $s in $studies: 
                            ${s.input.name};
                         #end for
"
            --nbreplicates "#for $s in $studies: 
                            ${s.nbreplicates};
                         #end for
"

            --fdr $fdr
            --result $top_table
            --htmloutput $result_html 
            --htmloutputpath $result_html.extra_files_path
            --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html    
    ]]>

    </command>

    <inputs>
         <repeat name="studies" title="Study results" min="2" default="2" help="DESeq2 Result file and number of replicate of the study">
             <param format="tabular" name="input" multiple="false" type="data" optional="false" label="DESeq2 result file" help="Must have the same number of row in each study"/>
             <param name="nbreplicates" type="integer" value="10"  label="Number of replicates" help="Number of replicates of the study"/>
         </repeat>
         <param name="fdr" type="float" value="0.05" label="FDR" min="0" max="1" help="Adjusted p-value threshold to be declared differentially expressed"/>
    </inputs>


    <outputs>
        <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
        <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/>
    </outputs>
    
    <tests>
        
    </tests>

    <help>
<![CDATA[ 
**What it does**
		
Given several DESeq2 results this tool runs a meta-analysis using the metaRNAseq R package.
		
**Inputs**

- At least 2 studies, and for each study

	- Results of DESeq2 study
	- Number of replicates of the study	
	
- A FDR Threshold for a gene to be declared differentially expressed		
	

**Results**
		
- Venn Diagram or upsetR diagram (when the number of studies is greater than 2) 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

It also generates a text file containing summarization of the results of each single analysis and meta-analysis. Potential conflicts between single analyses are indicated by zero values in the "signFC" column. 
]]>
    </help>

</tool>