--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/tools/ORApathwayEnrichment/ORApathwayEnrichment.xml	Wed Jul 26 15:33:45 2023 +0000
@@ -0,0 +1,77 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="1.5.0">
+  <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 :
+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)
+				Query	!Query
+	Target		a		b
+	!Target		c		d
+
+The probability of obtaining the set of value is computed as following:
+p = ((a+b)!(c+d)!(a+c)!(b+d)!)/(a!b!c!d!(a+b+c+d)!)
+
+The obtained p-value is then adjusted for multiple testing using one of the following methods:
+ - 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:1.5.0</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>
+  <citations/>
+</tool>