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comparison tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml @ 8:1274e2a62479 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
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7:1436e9cde9c9 8:1274e2a62479
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="MET4J_VERSION_TEST">
3 <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.
4 The fisher exact test compute the probability p to randomly get the given set of value.
5 This version compute the probability to get at least the given overlap between the given set and the given modality :
6 Sum the hypergeometric probability with increasing target/query intersection cardinality.
7
8 The hypergeometric probability is computed from the following contingency table entries.
9 (value in cells correspond to the marginal totals of each intersection groups)
10 Query !Query
11 Target a b
12 !Target c d
13
14 The probability of obtaining the set of value is computed as following:
15 p = ((a+b)!(c+d)!(a+c)!(b+d)!)/(a!b!c!d!(a+b+c+d)!)
16
17 The obtained p-value is then adjusted for multiple testing using one of the following methods:
18 - Bonferroni: adjusted p-value = p*n
19 - Benjamini-Hochberg: adjusted p-value = p*n/k
20 - Holm-Bonferroni: adjusted p-value = p*(n+1-k)
21 n : number of tests; k : pvalue rank</description>
22 <xrefs>
23 <xref type="bio.tools">met4j</xref>
24 </xrefs>
25 <requirements>
26 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
27 </requirements>
28 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != 'nan':
29 -th "$th"
30 #end if
31 -s "$sbml"
32 -i "$input"
33 #if str($corr):
34 -c "$corr"
35 #end if
36 -o "$outputFile"
37 ]]></command>
38 <inputs>
39 <param argument="-th" label="threshold to select significant pathways. No filtering if &lt;=0" name="th" optional="true" type="float" value="0.0"/>
40 <param argument="-s" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>
41 <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=""/>
42 <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">
43 <option value="Bonferroni">Bonferroni</option>
44 <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>
45 <option value="HolmBonferroni">HolmBonferroni</option>
46 </param>
47 </inputs>
48 <outputs>
49 <data format="tsv" name="outputFile"/>
50 </outputs>
51 <tests>
52 <test>
53 <param name="sbml" value="XF_network.sbml"/>
54 <param name="input" value="XF_network_C_NOI.txt"/>
55 <output name="outputFile">
56 <assert_contents>
57 <has_n_columns n="3"/>
58 <has_n_lines n="3"/>
59 </assert_contents>
60 </output>
61 </test>
62 <test>
63 <param name="sbml" value="XF_network.sbml"/>
64 <param name="input" value="XF_network_C_NOI.txt"/>
65 <param name="corr" value="HolmBonferroni"/>
66 <param name="th" value="0.005"/>
67 <output name="outputFile">
68 <assert_contents>
69 <has_n_columns n="3"/>
70 <has_n_lines n="2"/>
71 </assert_contents>
72 </output>
73 </test>
74 </tests>
75 <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.]]></help>
76 <citations/>
77 </tool>