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comparison tools/networkAnalysis/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
parents 6a112eaf8f38
children
comparison
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.0"> 2 <tool id="met4j_LoadPoint" name="LoadPoint" version="2.0.1">
3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description> 3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile" 12 -s "$sideCompoundFile"
13 #end if 13 #end if
28 <outputs> 28 <outputs>
29 <data format="tsv" name="outputPath"/> 29 <data format="tsv" name="outputPath"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
33
33 <param name="inputPath" value="toy_model.xml"/> 34 <param name="inputPath" value="toy_model.xml"/>
35
34 <output ftype="tsv" name="outputPath"> 36 <output ftype="tsv" name="outputPath">
37
35 <assert_contents> 38 <assert_contents>
39
36 <has_n_columns n="3"/> 40 <has_n_columns n="3"/>
41
37 <has_n_lines n="8"/> 42 <has_n_lines n="8"/>
43
38 </assert_contents> 44 </assert_contents>
45
39 </output> 46 </output>
47
40 </test> 48 </test>
41 </tests> 49 </tests>
42 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets. 50 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.
43 From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006): 51 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 : 52 For a given metabolic network, the load L on metabolite m can be defined as :