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comparison build/tools/LoadPoint/LoadPoint.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_LoadPoint" name="LoadPoint" version="1.3.0">
3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target.</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath"
11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile"
13 #end if
14 #if str($k):
15 -k "$k"
16 #end if
17 -o "$outputPath"
18 ]]></command>
19 <inputs>
20 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
21 <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
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">
23 <sanitizer invalid_char="_">
24 <valid initial="string.printable"/>
25 </sanitizer>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="tsv" name="outputPath"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="inputPath" value="toy_model.xml"/>
34 <output ftype="tsv" name="outputPath">
35 <assert_contents>
36 <has_n_columns n="3"/>
37 <has_n_lines n="8"/>
38 </assert_contents>
39 </output>
40 </test>
41 </tests>
42 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target.
43 From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006):
44 For a given metabolic network, the load L on metabolite m can be defined as :
45 ln [(pm/km)/(∑Mi=1Pi)/(∑Mi=1Ki)]
46 p is the number of shortest paths passing through a metabolite m;
47 k is the number of nearest neighbour links for m in the network;
48 P is the total number of shortest paths;
49 K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network).
50 Use of the logarithm makes the relevant values more distinguishable.]]></help>
51 <citations/>
52 </tool>