Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml @ 1:9b162ee6ff8e draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
author | metexplore |
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date | Mon, 27 Jun 2022 13:41:08 +0000 |
parents | dcd16521b969 |
children | e69a78624877 |
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0:dcd16521b969 | 1:9b162ee6ff8e |
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1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.11.0"> | 2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.12.0"> |
3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> | 3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</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:0.11.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container> |
9 </requirements> | 9 </requirements> |
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" |
11 -s "$sourcePath" | 11 -s "$sourcePath" |
12 -t "$targetPath" | 12 -t "$targetPath" |
13 #if str($sideCompoundFile) != 'None': | 13 #if str($sideCompoundFile) != 'None': |
16 $degree | 16 $degree |
17 #if str($weightFile) != 'None': | 17 #if str($weightFile) != 'None': |
18 -cw "$weightFile" | 18 -cw "$weightFile" |
19 #end if | 19 #end if |
20 $chemicalSim | 20 $chemicalSim |
21 $undirected | |
22 $asTable | |
21 #if str($k): | 23 #if str($k): |
22 -k "$k" | 24 -k "$k" |
23 #end if | 25 #end if |
24 $st | 26 $st |
25 -o "$outputPath" | 27 -o "$outputPath" |
30 <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> | 32 <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> |
31 <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> | 33 <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> |
32 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> | 34 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> |
33 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> | 35 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> |
34 <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> | 36 <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> |
37 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> | |
38 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> | |
35 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> | 39 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> |
36 <sanitizer invalid_char="_"> | 40 <sanitizer invalid_char="_"> |
37 <valid initial="string.printable"/> | 41 <valid initial="string.printable"/> |
38 </sanitizer> | 42 </sanitizer> |
39 </param> | 43 </param> |
65 Croes D, Couche F, Wodak SJ, et al. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006; 356:222–36. | 69 Croes D, Couche F, Wodak SJ, et al. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006; 356:222–36. |
66 Rahman SA, Advani P, Schunk R, et al. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005;21:1189–93. | 70 Rahman SA, Advani P, Schunk R, et al. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005;21:1189–93. |
67 Pertusi DA, Stine AE, Broadbelt LJ, et al. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics 2014;1–9. | 71 Pertusi DA, Stine AE, Broadbelt LJ, et al. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics 2014;1–9. |
68 McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003;19:1692–8. | 72 McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics 2003;19:1692–8. |
69 ]]></help> | 73 ]]></help> |
74 <citations/> | |
70 </tool> | 75 </tool> |