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comparison tools/networkAnalysis/ChokePoint/ChokePoint.xml @ 0:dcd16521b969 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ChokePoint" name="ChokePoint" version="0.11.0">
3 <description>Compute the Choke points of a metabolic network.</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:0.11.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile"
13 #end if
14 -o "$outputPath"
15 ]]></command>
16 <inputs>
17 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
18 <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
19 </inputs>
20 <outputs>
21 <data format="tsv" name="outputPath"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="inputPath" value="XF_network.sbml"/>
26 <output ftype="tsv" name="outputPath">
27 <assert_contents>
28 <has_n_lines n="202"/>
29 <has_n_columns n="3"/>
30 <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="1"/>
31 <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="1"/>
32 </assert_contents>
33 </output>
34 </test>
35 <test>
36 <param name="inputPath" value="XF_network.sbml"/>
37 <param name="sideCompoundFile" value="sides.txt"/>
38 <output ftype="tsv" name="outputPath">
39 <assert_contents>
40 <has_n_lines n="200"/>
41 <has_n_columns n="3"/>
42 <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="0"/>
43 <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="0"/>
44 </assert_contents>
45 </output>
46 </test>
47 </tests>
48 <help><![CDATA[Compute the Choke points of a metabolic network.
49 Load points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target
50 See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help>
51 </tool>