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comparison tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.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_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.0"> 2 <tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.1">
3 <description>Advanced creation of a compound graph representation of a SBML file content</description> 3 <description>Advanced creation of a compound graph representation of a SBML file content</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 convert.Sbml2CompoundGraph -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath"
11 #if str($inputSide) != 'None': 11 #if str($inputSide) != 'None':
12 -sc "$inputSide" 12 -sc "$inputSide"
13 #end if 13 #end if
52 <outputs> 52 <outputs>
53 <data format="txt" name="output"/> 53 <data format="txt" name="output"/>
54 </outputs> 54 </outputs>
55 <tests> 55 <tests>
56 <test> 56 <test>
57
57 <param name="inputPath" value="XF_network.sbml"/> 58 <param name="inputPath" value="XF_network.sbml"/>
59
58 <param name="inputSide" value="XF_network_C_Side.tab"/> 60 <param name="inputSide" value="XF_network_C_Side.tab"/>
61
59 <param name="format" value="gml"/> 62 <param name="format" value="gml"/>
63
60 <output name="output"> 64 <output name="output">
65
61 <assert_contents> 66 <assert_contents>
67
62 <has_line_matching expression=".*node.*" n="1101"/> 68 <has_line_matching expression=".*node.*" n="1101"/>
69
63 <has_line_matching expression=".*edge.*" n="5581"/> 70 <has_line_matching expression=".*edge.*" n="5581"/>
71
64 </assert_contents> 72 </assert_contents>
73
65 </output> 74 </output>
75
66 </test> 76 </test>
67 <test> 77 <test>
78
68 <param name="inputPath" value="XF_network.sbml"/> 79 <param name="inputPath" value="XF_network.sbml"/>
80
69 <param name="inputSide" value="XF_network_C_Side.tab"/> 81 <param name="inputSide" value="XF_network_C_Side.tab"/>
82
70 <param name="undirected" value="true"/> 83 <param name="undirected" value="true"/>
84
71 <param name="computeWeight" value="true"/> 85 <param name="computeWeight" value="true"/>
86
72 <param name="removeIsolated" value="true"/> 87 <param name="removeIsolated" value="true"/>
88
73 <param name="degree" value="true"/> 89 <param name="degree" value="true"/>
90
74 <param name="mergingStrat" value="by_id"/> 91 <param name="mergingStrat" value="by_id"/>
92
75 <param name="format" value="gml"/> 93 <param name="format" value="gml"/>
94
76 <output name="output"> 95 <output name="output">
96
77 <assert_contents> 97 <assert_contents>
98
78 <has_line_matching expression=".*node.*" n="793"/> 99 <has_line_matching expression=".*node.*" n="793"/>
100
79 <has_line_matching expression=".*edge.*" n="9372"/> 101 <has_line_matching expression=".*edge.*" n="9372"/>
102
80 </assert_contents> 103 </assert_contents>
104
81 </output> 105 </output>
106
82 </test> 107 </test>
83 </tests> 108 </tests>
84 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. 109 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.
85 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations. 110 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
86 In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help> 111 In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>