--- a/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,12 +1,286 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="MET4J_VERSION_TEST">
-  <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.
-The fisher exact test compute the probability p to randomly get the given set of value. 
-This version compute the probability to get at least the given overlap between the given set and the given modality :
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="develop">
+  <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != 'nan':
+ -th "$th"
+#end if
+ -i "$sbml"
+ -d "$input"
+#if str($corr):
+ -c "$corr"
+#end if
+ -o "$outputFile"
+]]></command>
+  <inputs>
+    <param argument="-th" label="threshold to select significant pathways. No filtering if &lt;=0" name="th" optional="true" type="float" value="0.0"/>
+    <param argument="-i" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>
+    <param argument="-d" format="tsv" label="Input data : Compounds of interest file, as one SBML specie identifier per line" name="input" optional="false" type="data" value=""/>
+    <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">
+      <option value="Bonferroni">Bonferroni</option>
+      <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>
+      <option value="HolmBonferroni">HolmBonferroni</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputFile"/>
+  </outputs>
+  <tests>
+    <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="sbml" value="XF_network.sbml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="input" value="XF_network_C_NOI.txt"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <output name="outputFile">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_columns n="3"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="3"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    </test>
+    <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="sbml" value="XF_network.sbml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="input" value="XF_network_C_NOI.txt"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="corr" value="HolmBonferroni"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="th" value="0.005"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <output name="outputFile">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_columns n="3"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="2"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    </test>
+  </tests>
+  <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.
+The fisher exact test computes the probability p to randomly get the given set of values. 
+This version computes the probability to get at least the given overlap between the given set and the given modality :
 Sum the hypergeometric probability with increasing target/query intersection cardinality.
 
 The hypergeometric probability is computed from the following contingency table entries.
-(value in cells correspond to the marginal totals of each intersection groups)
+(values in cells correspond to the marginal totals of each intersection groups)
 				Query	!Query
 	Target		a		b
 	!Target		c		d
@@ -18,60 +292,6 @@
  - Bonferroni: adjusted p-value = p*n
  - Benjamini-Hochberg: adjusted p-value = p*n/k
  - Holm-Bonferroni: adjusted p-value = p*(n+1-k)
-n : number of tests; k : pvalue rank</description>
-  <xrefs>
-    <xref type="bio.tools">met4j</xref>
-  </xrefs>
-  <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != 'nan':
- -th "$th"
-#end if
- -s "$sbml"
- -i "$input"
-#if str($corr):
- -c "$corr"
-#end if
- -o "$outputFile"
-]]></command>
-  <inputs>
-    <param argument="-th" label="threshold to select significant pathways. No filtering if &lt;=0" name="th" optional="true" type="float" value="0.0"/>
-    <param argument="-s" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>
-    <param argument="-i" format="tsv" label="Input data : Compounds of interest file, as one SBML specie identifier per line" name="input" optional="false" type="data" value=""/>
-    <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">
-      <option value="Bonferroni">Bonferroni</option>
-      <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>
-      <option value="HolmBonferroni">HolmBonferroni</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="tsv" name="outputFile"/>
-  </outputs>
-  <tests>
-  <test>
-      <param name="sbml" value="XF_network.sbml"/>
-      <param name="input" value="XF_network_C_NOI.txt"/>
-      <output name="outputFile">
-        <assert_contents>
-          <has_n_columns n="3"/>
-          <has_n_lines n="3"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="sbml" value="XF_network.sbml"/>
-      <param name="input" value="XF_network_C_NOI.txt"/>
-      <param name="corr" value="HolmBonferroni"/>
-      <param name="th" value="0.005"/>
-      <output name="outputFile">
-        <assert_contents>
-          <has_n_columns n="3"/>
-          <has_n_lines n="2"/>
-        </assert_contents>
-      </output>
-    </test>
-    </tests>
-  <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.]]></help>
+n : number of tests; k : pvalue rank]]></help>
   <citations/>
 </tool>