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comparison tools/mapping/ORApathwayEnrichment/ORApathwayEnrichment.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 1274e2a62479
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_ORApathwayEnrichment" name="ORApathwayEnrichment" version="develop">
3 <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test. 3 <description>Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.</description>
4 The fisher exact test compute the probability p to randomly get the given set of value. 4 <xrefs>
5 This version compute the probability to get at least the given overlap between the given set and the given modality : 5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh mapping.ORApathwayEnrichment#if str($th) != 'nan':
11 -th "$th"
12 #end if
13 -i "$sbml"
14 -d "$input"
15 #if str($corr):
16 -c "$corr"
17 #end if
18 -o "$outputFile"
19 ]]></command>
20 <inputs>
21 <param argument="-th" label="threshold to select significant pathways. No filtering if &lt;=0" name="th" optional="true" type="float" value="0.0"/>
22 <param argument="-i" format="sbml" label="Input model : SBML file with pathway annotation" name="sbml" optional="false" type="data" value=""/>
23 <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=""/>
24 <param argument="-c" label="Method for multiple testing p-value adjustment." name="corr" optional="true" type="select" value="BenjaminiHochberg">
25 <option value="Bonferroni">Bonferroni</option>
26 <option selected="true" value="BenjaminiHochberg">BenjaminiHochberg</option>
27 <option value="HolmBonferroni">HolmBonferroni</option>
28 </param>
29 </inputs>
30 <outputs>
31 <data format="tsv" name="outputFile"/>
32 </outputs>
33 <tests>
34 <test>
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46 <param name="sbml" value="XF_network.sbml"/>
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58 <param name="input" value="XF_network_C_NOI.txt"/>
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70 <output name="outputFile">
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82 <assert_contents>
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94 <has_n_columns n="3"/>
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106 <has_n_lines n="3"/>
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118 </assert_contents>
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130 </output>
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142 </test>
143 <test>
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155 <param name="sbml" value="XF_network.sbml"/>
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167 <param name="input" value="XF_network_C_NOI.txt"/>
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179 <param name="corr" value="HolmBonferroni"/>
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191 <param name="th" value="0.005"/>
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203 <output name="outputFile">
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215 <assert_contents>
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227 <has_n_columns n="3"/>
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239 <has_n_lines n="2"/>
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251 </assert_contents>
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263 </output>
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275 </test>
276 </tests>
277 <help><![CDATA[Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.
278 The fisher exact test computes the probability p to randomly get the given set of values.
279 This version computes 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. 280 Sum the hypergeometric probability with increasing target/query intersection cardinality.
7 281
8 The hypergeometric probability is computed from the following contingency table entries. 282 The hypergeometric probability is computed from the following contingency table entries.
9 (value in cells correspond to the marginal totals of each intersection groups) 283 (values in cells correspond to the marginal totals of each intersection groups)
10 Query !Query 284 Query !Query
11 Target a b 285 Target a b
12 !Target c d 286 !Target c d
13 287
14 The probability of obtaining the set of value is computed as following: 288 The probability of obtaining the set of value is computed as following:
16 290
17 The obtained p-value is then adjusted for multiple testing using one of the following methods: 291 The obtained p-value is then adjusted for multiple testing using one of the following methods:
18 - Bonferroni: adjusted p-value = p*n 292 - Bonferroni: adjusted p-value = p*n
19 - Benjamini-Hochberg: adjusted p-value = p*n/k 293 - Benjamini-Hochberg: adjusted p-value = p*n/k
20 - Holm-Bonferroni: adjusted p-value = p*(n+1-k) 294 - Holm-Bonferroni: adjusted p-value = p*(n+1-k)
21 n : number of tests; k : pvalue rank</description> 295 n : number of tests; k : pvalue rank]]></help>
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/> 296 <citations/>
77 </tool> 297 </tool>