Mercurial > repos > metexplore > met4j

comparison tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml @ 9:0976a6257300 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
equal deleted inserted replaced
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_ScopeNetwork" name="ScopeNetwork" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="develop">
3 <description>Perform a network expansion from a set of compound seeds to create a scope network</description> 3 <description>Perform a network expansion from a set of compound seeds to create a scope 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: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.ScopeNetwork -i "$sbmlFilePath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
11 -s "$seedsFilePath" 11 -s "$seedsFilePath"
12 #if str($sideCompoundFile) != 'None': 12 #if str($sideCompoundFile) != 'None':
13 -sc "$sideCompoundFile" 13 -sc "$sideCompoundFile"
15 $includeSides 15 $includeSides
16 #if str($reactionToIgnoreFile) != 'None': 16 #if str($reactionToIgnoreFile) != 'None':
17 -ir "$reactionToIgnoreFile" 17 -ir "$reactionToIgnoreFile"
18 #end if 18 #end if
19 $trace 19 $trace
20 $asTable 20 #if str($format):
21 -f "$format"
22 #end if
21 -o "$output" 23 -o "$output"
22 ]]></command> 24 ]]></command>
23 <inputs> 25 <inputs>
24 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/> 26 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
25 <param argument="-s" format="txt" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/> 27 <param argument="-s" format="txt" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/>
26 <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous side compounds to be considered available by default but ignored during expansion" name="sideCompoundFile" optional="true" type="data" value=""/> 28 <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous side compounds to be considered available by default but ignored during expansion" name="sideCompoundFile" optional="true" type="data" value=""/>
27 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/> 29 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/>
28 <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/> 30 <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
29 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/> 31 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/>
30 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> 32 <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">
33 <option value="gml">gml</option>
34 <option selected="true" value="tab">tab</option>
35 <option value="nodeList">nodeList</option>
36 <option value="json">json</option>
37 <option value="matrix">matrix</option>
38 </param>
31 </inputs> 39 </inputs>
32 <outputs> 40 <outputs>
33 <data format="gml" name="output"/> 41 <data format="txt" name="output"/>
34 </outputs> 42 </outputs>
35 <tests> 43 <tests>
36 <test> 44 <test>
45
46
47
37 <param name="sbmlFilePath" value="toy_model.xml"/> 48 <param name="sbmlFilePath" value="toy_model.xml"/>
49
50
51
38 <param name="seedsFilePath" value="seeds.txt"/> 52 <param name="seedsFilePath" value="seeds.txt"/>
53
54
55
39 <param name="sideCompoundFile" value="sides.txt"/> 56 <param name="sideCompoundFile" value="sides.txt"/>
40 <output ftype="gml" name="output"> 57
58
59
60 <param name="format" value="gml"/>
61
62
63
64 <output ftype="txt" name="output">
65
66
67
41 <assert_contents> 68 <assert_contents>
69
70
71
42 <has_line_matching expression=".*node.*" n="9"/> 72 <has_line_matching expression=".*node.*" n="9"/>
73
74
75
43 <has_line_matching expression=".*edge.*" n="11"/> 76 <has_line_matching expression=".*edge.*" n="11"/>
77
78
79
44 </assert_contents> 80 </assert_contents>
81
82
83
45 </output> 84 </output>
85
86
87
46 </test> 88 </test>
47 </tests> 89 </tests>
48 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network 90 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
49 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction 91 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction]]></help>
50 For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help> 92 <citations>
51 <citations/> 93 <citation type="doi">10.1007/s00239-005-0027-1</citation>
94 </citations>
52 </tool> 95 </tool>