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comparison tools/networkAnalysis/CompoundNet/CompoundNet.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
| author | metexplore |
|---|---|
| date | Fri, 10 Jun 2022 10:31:34 +0000 |
| parents | |
| children | 9b162ee6ff8e |
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| -1:000000000000 | 0:dcd16521b969 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_CompoundNet" name="CompoundNet" version="0.11.0"> | |
| 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:0.11.0</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="" 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 "xxx_y" 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="" 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 degree² 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 </tool> |