diff LoadPoint.xml @ 0:5aafcd772390 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/LoadPoint.xml	Thu Mar 13 15:47:44 2025 +0000
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_LoadPoint" name="LoadPoint" version="@TOOL_VERSION@">
+  <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</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.LoadPoint -i "$inputPath"
+#if str($sideCompoundFile) != 'None':
+ -s "$sideCompoundFile"
+#end if
+#if str($k):
+ -k "$k"
+#end if
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-k" label="Number of alternative paths to consider between a pair of connected metabolites" name="k" optional="true" type="text" value="1">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputPath"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="inputPath" value="toy_model.xml"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_columns n="3"/>
+          <has_n_lines n="8"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.
+From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006):
+For a given metabolic network, the load L on metabolite m can be defined as :
+ln [(pm/km)/(∑Mi=1Pi)/(∑Mi=1Ki)]
+p is the number of shortest paths passing through a metabolite m;
+k is the number of nearest neighbour links for m in the network;
+P is the total number of shortest paths;
+K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network).
+Use of the logarithm makes the relevant values more distinguishable.
+@ATTRIBUTION@]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btl181</citation>
+  </citations>
+</tool>