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

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