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annotate build/tools/MetaboRank/MetaboRank.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_MetaboRank" name="MetaboRank" version="2.0.1">
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3 <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath"
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11 -s "$seedsFilePath"
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12 #if str($edgeWeightsFilePaths) != 'None':
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13 -w "$edgeWeightsFilePaths"
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14 #end if
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15 #if str($inputSide) != 'None':
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16 -sc "$inputSide"
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17 #end if
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18 #if str($maxNbOfIter):
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19 -max "$maxNbOfIter"
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20 #end if
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21 #if str($tolerance) != 'nan':
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22 -t "$tolerance"
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23 #end if
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24 #if str($dampingFactor) != 'nan':
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25 -d "$dampingFactor"
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26 #end if
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27 -o "$output"
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28 ]]></command>
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29 <inputs>
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30 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing centrality, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
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31 <param argument="-s" format="tsv" label="input seeds file: tabulated file containing node of interest ids and weight" name="seedsFilePath" optional="false" type="data" value=""/>
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32 <param argument="-w" format="tsv" label="input edge weight file: (recommended) path to file containing edges' weights. Will be normalized as transition probabilities" name="edgeWeightsFilePaths" optional="true" type="data" value=""/>
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33 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
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34 <param argument="-max" label="maximal number of iteration" name="maxNbOfIter" optional="true" type="text" value="15000">
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35 <sanitizer invalid_char="_">
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36 <valid initial="string.printable"/>
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37 </sanitizer>
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38 </param>
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39 <param argument="-t" label="convergence tolerance" name="tolerance" optional="true" type="float" value="0.001"/>
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40 <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/>
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41 </inputs>
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42 <outputs>
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43 <data format="tsv" name="output"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47
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48 <param name="sbmlFilePath" value="XF_network.sbml"/>
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50 <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
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52 <param name="inputSide" value="XF_network_C_Side.tab"/>
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54 <output name="output">
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56 <assert_contents>
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58 <has_n_lines n="1100"/>
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60 <has_n_columns n="11"/>
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62 </assert_contents>
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64 </output>
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66 </test>
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67 </tests>
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68 <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
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69 The MetaboRank takes a metabolic network and a list of compounds of interest, and provide a score of relevance for all of the other compounds in the network.
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70 The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.
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71 It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.
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72 For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker.
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73 See publication for more information.]]></help>
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74 <citations>
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75 <citation type="doi">10.1093/bioinformatics/bty577</citation>
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76 </citations>
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77 </tool>