--- a/MetaRNAseq.xml	Thu Mar 22 11:16:24 2018 -0400
+++ b/MetaRNAseq.xml	Tue Jun 26 08:54:45 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0">
+<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0">
 
     <description>Performs meta-analysis thanks to metaRNAseq</description>
 
@@ -10,6 +10,7 @@
         <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>
@@ -19,21 +20,40 @@
 
     <command>
 
-    <![CDATA[ 	
+<![CDATA[   
         Rscript 
         ${__tool_directory__}/MetaRNASeq.R 
-            --input "#for $input in $inputs# $input;$input.name, #end for#"
+            --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	
-    ]]>	
+            --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html    
+    ]]>
+
     </command>
 
     <inputs>
-        <param format="tabular" name="inputs" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
+         <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}"/>
@@ -44,7 +64,31 @@
     </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>