diff MetaboRank.xml @ 0:f41a5255a7ec draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaboRank.xml	Thu Mar 13 15:47:54 2025 +0000
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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_MetaboRank" name="MetaboRank" version="@TOOL_VERSION@">
+  <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis.MetaboRank -i "$sbmlFilePath"
+ -s "$seedsFilePath"
+#if str($edgeWeightsFilePaths) != 'None':
+ -w "$edgeWeightsFilePaths"
+#end if
+#if str($inputSide) != 'None':
+ -sc "$inputSide"
+#end if
+#if str($maxNbOfIter):
+ -max "$maxNbOfIter"
+#end if
+#if str($tolerance) != 'nan':
+ -t "$tolerance"
+#end if
+#if str($dampingFactor) != 'nan':
+ -d "$dampingFactor"
+#end if
+ -o "$output"
+]]></command>
+  <inputs>
+    <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=""/>
+    <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=""/>
+    <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=""/>
+    <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
+    <param argument="-max" label="maximal number of iteration" name="maxNbOfIter" optional="true" type="text" value="15000">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-t" label="convergence tolerance" name="tolerance" optional="true" type="float" value="0.001"/>
+    <param argument="-d" label="damping factor" name="dampingFactor" optional="true" type="float" value="0.85"/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="sbmlFilePath" value="XF_network.sbml"/>
+      <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
+      <param name="inputSide" value="XF_network_C_Side.tab"/>
+      <output name="output">
+        <assert_contents>
+          <has_n_lines n="1100"/>
+          <has_n_columns n="11"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
+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.
+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.
+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.
+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.
+See publication for more information.
+@ATTRIBUTION@]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/bty577</citation>
+  </citations>
+</tool>