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comparison tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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children 6a112eaf8f38
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="develop">
3 <description>Advanced creation of a compound graph representation of a SBML file content</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:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath"
11 #if str($inputSide) != 'None':
12 -sc "$inputSide"
13 #end if
14 #if str($mergingStrat):
15 -mc "$mergingStrat"
16 #end if
17 $mergeEdges
18 $removeIsolated
19 $degree
20 #if str($weightFile) != 'None':
21 -cw "$weightFile"
22 #end if
23 $undirected
24 $computeWeight
25 #if str($format):
26 -f "$format"
27 #end if
28 -o "$output"
29 ]]></command>
30 <inputs>
31 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
32 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
33 <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
34 <option selected="true" value="no">no</option>
35 <option value="by_name">by_name</option>
36 <option value="by_id">by_id</option>
37 </param>
38 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
39 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
40 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/>
41 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
42 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
43 <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
44 <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
45 <option value="gml">gml</option>
46 <option selected="true" value="tab">tab</option>
47 <option value="nodeList">nodeList</option>
48 <option value="json">json</option>
49 <option value="matrix">matrix</option>
50 </param>
51 </inputs>
52 <outputs>
53 <data format="txt" name="output"/>
54 </outputs>
55 <tests>
56 <test>
57
58
59
60 <param name="inputPath" value="XF_network.sbml"/>
61
62
63
64 <param name="inputSide" value="XF_network_C_Side.tab"/>
65
66
67
68 <param name="format" value="gml"/>
69
70
71
72 <output name="output">
73
74
75
76 <assert_contents>
77
78
79
80 <has_line_matching expression=".*node.*" n="1101"/>
81
82
83
84 <has_line_matching expression=".*edge.*" n="5581"/>
85
86
87
88 </assert_contents>
89
90
91
92 </output>
93
94
95
96 </test>
97 <test>
98
99
100
101 <param name="inputPath" value="XF_network.sbml"/>
102
103
104
105 <param name="inputSide" value="XF_network_C_Side.tab"/>
106
107
108
109 <param name="undirected" value="true"/>
110
111
112
113 <param name="computeWeight" value="true"/>
114
115
116
117 <param name="removeIsolated" value="true"/>
118
119
120
121 <param name="degree" value="true"/>
122
123
124
125 <param name="mergingStrat" value="by_id"/>
126
127
128
129 <param name="format" value="gml"/>
130
131
132
133 <output name="output">
134
135
136
137 <assert_contents>
138
139
140
141 <has_line_matching expression=".*node.*" n="793"/>
142
143
144
145 <has_line_matching expression=".*edge.*" n="9372"/>
146
147
148
149 </assert_contents>
150
151
152
153 </output>
154
155
156
157 </test>
158 </tests>
159 <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.
160 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.
161 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>
162 <citations/>
163 </tool>