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annotate build/tools/LoadPoint/LoadPoint.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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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.1">
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3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</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.LoadPoint -i "$inputPath"
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11 #if str($sideCompoundFile) != 'None':
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12 -s "$sideCompoundFile"
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13 #end if
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14 #if str($k):
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15 -k "$k"
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16 #end if
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17 -o "$outputPath"
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18 ]]></command>
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19 <inputs>
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20 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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21 <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
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22 <param argument="-k" label="Number of alternative paths to consider between a pair of connected metabolites" name="k" optional="true" type="text" value="1">
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23 <sanitizer invalid_char="_">
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24 <valid initial="string.printable"/>
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25 </sanitizer>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="tsv" name="outputPath"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33
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34 <param name="inputPath" value="toy_model.xml"/>
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36 <output ftype="tsv" name="outputPath">
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38 <assert_contents>
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40 <has_n_columns n="3"/>
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42 <has_n_lines n="8"/>
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44 </assert_contents>
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45
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46 </output>
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47
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48 </test>
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49 </tests>
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50 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.
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51 From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006):
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52 For a given metabolic network, the load L on metabolite m can be defined as :
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53 ln [(pm/km)/(∑Mi=1Pi)/(∑Mi=1Ki)]
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54 p is the number of shortest paths passing through a metabolite m;
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55 k is the number of nearest neighbour links for m in the network;
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56 P is the total number of shortest paths;
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57 K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network).
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58 Use of the logarithm makes the relevant values more distinguishable.]]></help>
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59 <citations>
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60 <citation type="doi">10.1093/bioinformatics/btl181</citation>
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61 </citations>
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62 </tool>