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comparison build/tools/ChokePoint/ChokePoint.xml @ 7:1436e9cde9c9 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
parents 7a6f2380fc1d
children 1274e2a62479
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6:7a6f2380fc1d 7:1436e9cde9c9
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ChokePoint" name="ChokePoint" version="1.3.0"> 2 <tool id="met4j_ChokePoint" name="ChokePoint" version="1.4.0">
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:1.3.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</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($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile"
13 #end if
14 -o "$outputPath" 11 -o "$outputPath"
15 ]]></command> 12 ]]></command>
16 <inputs> 13 <inputs>
17 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 14 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
18 <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
19 </inputs> 15 </inputs>
20 <outputs> 16 <outputs>
21 <data format="tsv" name="outputPath"/> 17 <data format="tsv" name="outputPath"/>
22 </outputs> 18 </outputs>
23 <tests> 19 <tests>
24 <test> 20 <test>
25 <param name="inputPath" value="XF_network.sbml"/> 21 <param name="inputPath" value="XF_network.sbml"/>
26 <output ftype="tsv" name="outputPath"> 22 <output ftype="tsv" name="outputPath">
27 <assert_contents> 23 <assert_contents>
28 <has_n_lines n="202"/> 24 <has_n_lines n="695"/>
29 <has_n_columns n="3"/> 25 <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"/> 26 <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"/> 27 <has_line_matching expression="R_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --&gt; M_ac_c \+ M_gam6p_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="1" negate="true"/>
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> 28 </assert_contents>
45 </output> 29 </output>
46 </test> 30 </test>
47 </tests> 31 </tests>
48 <help><![CDATA[Compute the Choke points of a metabolic network. 32 <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 33 Choke 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> 34 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/> 35 <citations/>
52 </tool> 36 </tool>