Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml @ 8:1274e2a62479 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
| author | metexplore |
|---|---|
| date | Wed, 26 Jul 2023 15:33:45 +0000 |
| parents | 7a6f2380fc1d |
| children | 0976a6257300 |
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| 7:1436e9cde9c9 | 8:1274e2a62479 |
|---|---|
| 11 -s "$sourcePath" | 11 -s "$sourcePath" |
| 12 $undirected | 12 $undirected |
| 13 $asTable | 13 $asTable |
| 14 -t "$targetPath" | 14 -t "$targetPath" |
| 15 -sc "$sideCompoundFile" | 15 -sc "$sideCompoundFile" |
| 16 #if str($rExclude) != 'None': | |
| 17 -re "$rExclude" | |
| 18 #end if | |
| 16 #if str($weightFile) != 'None': | 19 #if str($weightFile) != 'None': |
| 17 -cw "$weightFile" | 20 -cw "$weightFile" |
| 18 #end if | 21 #end if |
| 19 #if str($k): | 22 #if str($k): |
| 20 -k "$k" | 23 -k "$k" |
| 27 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> | 30 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> |
| 28 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> | 31 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> |
| 29 <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="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> |
| 30 <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=""/> |
| 31 <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> | 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="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/> | |
| 32 <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" 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=""/> |
| 33 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> | 37 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> |
| 34 <sanitizer invalid_char="_"> | 38 <sanitizer invalid_char="_"> |
| 35 <valid initial="string.printable"/> | 39 <valid initial="string.printable"/> |
| 36 </sanitizer> | 40 </sanitizer> |