Mercurial > repos > iuc > isoformswitchanalyzer
comparison IsoformSwitchAnalyzeR.R @ 3:02a77166b29a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 44cb89c86b7a48993b6987a3a40129782fd7a093
| author | iuc |
|---|---|
| date | Wed, 24 May 2023 13:33:53 +0000 |
| parents | 2b0a6af4b85e |
| children | 512d6462f2ce |
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| 2:2b0a6af4b85e | 3:02a77166b29a |
|---|---|
| 512 onlySigIsoforms = args$onlySigIsoforms, | 512 onlySigIsoforms = args$onlySigIsoforms, |
| 513 keepIsoformInAllConditions = args$keepIsoformInAllConditions2, | 513 keepIsoformInAllConditions = args$keepIsoformInAllConditions2, |
| 514 showProgress = TRUE, | 514 showProgress = TRUE, |
| 515 ) | 515 ) |
| 516 | 516 |
| 517 if (!is.null(args$stringtieAnnotation)) { | 517 # Analyze missing annotated isoforms by default |
| 518 SwitchList <- analyzeNovelIsoformORF( | 518 SwitchList <- analyzeNovelIsoformORF( |
| 519 SwitchList, | 519 SwitchList, |
| 520 analysisAllIsoformsWithoutORF = TRUE, | 520 analysisAllIsoformsWithoutORF = TRUE, |
| 521 minORFlength = args$minORFlength, | 521 minORFlength = args$minORFlength, |
| 522 orfMethod = args$orfMethod, | 522 orfMethod = args$orfMethod, |
| 523 PTCDistance = args$PTCDistance, | 523 PTCDistance = args$PTCDistance, |
| 524 startCodons = "ATG", | 524 startCodons = "ATG", |
| 525 stopCodons = c("TAA", "TAG", "TGA"), | 525 stopCodons = c("TAA", "TAG", "TGA"), |
| 526 showProgress = TRUE, | 526 showProgress = TRUE, |
| 527 ) | 527 ) |
| 528 } | |
| 529 | 528 |
| 530 ### Extract Sequences | 529 ### Extract Sequences |
| 531 SwitchList <- extractSequence( | 530 SwitchList <- extractSequence( |
| 532 SwitchList, | 531 SwitchList, |
| 533 onlySwitchingGenes = args$onlySwitchingGenes, | 532 onlySwitchingGenes = args$onlySwitchingGenes, |