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comparison tools/networkAnalysis/ChokePoint/ChokePoint.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
parents 35c9abcd8934
children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ChokePoint" name="ChokePoint" version="1.2.1"> 2 <tool id="met4j_ChokePoint" name="ChokePoint" version="MET4J_VERSION_TEST">
3 <description>Compute the Choke points of a metabolic network.</description> 3 <description>Compute the Choke points of a metabolic network.</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:1.2.1</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile" 12 -s "$sideCompoundFile"
13 #end if 13 #end if
20 <outputs> 20 <outputs>
21 <data format="tsv" name="outputPath"/> 21 <data format="tsv" name="outputPath"/>
22 </outputs> 22 </outputs>
23 <tests> 23 <tests>
24 <test> 24 <test>
25 <param name="inputPath" value="XF_network.sbml"/> 25 <param name="inputPath" value="XF_network.sbml"/>
26 <output ftype="tsv" name="outputPath"> 26 <output ftype="tsv" name="outputPath">
27 <assert_contents> 27 <assert_contents>
28 <has_n_lines n="202"/> 28 <has_n_lines n="202"/>
29 <has_n_columns n="3"/> 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"/> 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"/> 31 <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="1"/>
32 </assert_contents> 32 </assert_contents>
33 </output> 33 </output>
34 </test> 34 </test>
35 <test> 35 <test>
36 <param name="inputPath" value="XF_network.sbml"/> 36 <param name="inputPath" value="XF_network.sbml"/>
37 <param name="sideCompoundFile" value="sides.txt"/> 37 <param name="sideCompoundFile" value="sides.txt"/>
38 <output ftype="tsv" name="outputPath"> 38 <output ftype="tsv" name="outputPath">
39 <assert_contents> 39 <assert_contents>
40 <has_n_lines n="200"/> 40 <has_n_lines n="200"/>
41 <has_n_columns n="3"/> 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"/> 42 <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="1" negate="true"/>
43 <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="0"/> 43 <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="1" negate="true"/>
44 </assert_contents> 44 </assert_contents>
45 </output> 45 </output>
46 </test> 46 </test>
47 </tests> 47 </tests>
48 <help><![CDATA[Compute the Choke points of a metabolic network. 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 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> 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 <citations/> 51 <citations/>