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comparison tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.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
parents 7a6f2380fc1d
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="develop">
3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> 3 <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
11 -s "$sourcePath" 11 -s "$sourcePath"
12 -t "$targetPath" 12 -t "$targetPath"
13 $undirected 13 $undirected
14 $asTable
15 -sc "$sideCompoundFile" 14 -sc "$sideCompoundFile"
16 #if str($blkdReactionFile) != 'None': 15 #if str($blkdReactionFile) != 'None':
17 -br "$blkdReactionFile" 16 -br "$blkdReactionFile"
18 #end if 17 #end if
19 #if str($weightFile) != 'None': 18 #if str($weightFile) != 'None':
21 #end if 20 #end if
22 #if str($k): 21 #if str($k):
23 -k "$k" 22 -k "$k"
24 #end if 23 #end if
25 $st 24 $st
26 -o "$outputPath" 25 #if str($format):
26 -f "$format"
27 #end if
28 -o "$output"
27 ]]></command> 29 ]]></command>
28 <inputs> 30 <inputs>
29 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 31 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
30 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> 32 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
31 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> 33 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
32 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 34 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
33 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
34 <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> 35 <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
35 <param argument="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" type="data" value=""/> 36 <param argument="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" type="data" value=""/>
36 <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/> 37 <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/>
37 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> 38 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
38 <sanitizer invalid_char="_"> 39 <sanitizer invalid_char="_">
39 <valid initial="string.printable"/> 40 <valid initial="string.printable"/>
40 </sanitizer> 41 </sanitizer>
41 </param> 42 </param>
42 <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/> 43 <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" 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>
43 </inputs> 51 </inputs>
44 <outputs> 52 <outputs>
45 <data format="gml" name="outputPath"/> 53 <data format="txt" name="output"/>
46 </outputs> 54 </outputs>
47 <tests> 55 <tests>
48 <test> 56 <test>
49 <param name="inputPath" value="toy_model.xml"/> 57
50 <param name="sourcePath" value="seeds.txt"/> 58
51 <param name="targetPath" value="targets.txt"/> 59
52 <param name="sideCompoundFile" value="sc.txt"/> 60 <param name="inputPath" value="toy_model.xml"/>
53 <output ftype="gml" name="outputPath"> 61
54 <assert_contents> 62
55 <has_line_matching expression=".*node.*" n="5"/> 63
56 <has_line_matching expression=".*edge.*" n="4"/> 64 <param name="sourcePath" value="seeds.txt"/>
57 </assert_contents> 65
58 </output> 66
59 </test> 67
68 <param name="targetPath" value="targets.txt"/>
69
70
71
72 <param name="sideCompoundFile" value="sc.txt"/>
73
74
75
76 <param name="format" value="gml"/>
77
78
79
80 <output ftype="txt" name="output">
81
82
83
84 <assert_contents>
85
86
87
88 <has_line_matching expression=".*node.*" n="5"/>
89
90
91
92 <has_line_matching expression=".*edge.*" n="4"/>
93
94
95
96 </assert_contents>
97
98
99
100 </output>
101
102
103
104 </test>
60 </tests> 105 </tests>
61 <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids. 106 <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
62 The subnetwork corresponds to part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list. 107 The subnetwork corresponds to the part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list.
63 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help> 108 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help>
64 <citations/> 109 <citations/>
65 </tool> 110 </tool>