<?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>