comparison build/tools/CompoundNet/CompoundNet.xml @ 6:7a6f2380fc1d draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_CompoundNet" name="CompoundNet" version="1.3.0">
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:1.3.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
11 #if str($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 $asMatrix
26 -o "$outputPath"
27 ]]></command>
28 <inputs>
29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
30 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
31 <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">
32 <option selected="true" value="no">no</option>
33 <option value="by_name">by_name</option>
34 <option value="by_id">by_id</option>
35 </param>
36 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
37 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
38 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/>
39 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
40 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
41 <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"/>
42 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
43 </inputs>
44 <outputs>
45 <data format="gml" name="outputPath"/>
46 </outputs>
47 <tests>
48 <test>
49 <param name="inputPath" value="XF_network.sbml"/>
50 <param name="inputSide" value="XF_network_C_Side.tab"/>
51 <output name="outputPath">
52 <assert_contents>
53 <has_line_matching expression=".*node.*" n="1101"/>
54 <has_line_matching expression=".*edge.*" n="5581"/>
55 </assert_contents>
56 </output>
57 </test>
58 <test>
59 <param name="inputPath" value="XF_network.sbml"/>
60 <param name="inputSide" value="XF_network_C_Side.tab"/>
61 <param name="undirected" value="true"/>
62 <param name="computeWeight" value="true"/>
63 <param name="removeIsolated" value="true"/>
64 <param name="degree" value="true"/>
65 <param name="mergingStrat" value="by_id"/>
66 <output name="outputPath">
67 <assert_contents>
68 <has_line_matching expression=".*node.*" n="793"/>
69 <has_line_matching expression=".*edge.*" n="9372"/>
70 </assert_contents>
71 </output>
72 </test>
73 </tests>
74 <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.
75 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.
76 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 degreeĀ² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>
77 <citations/>
78 </tool>