comparison IsoformSwitchAnalyzeR.R @ 3:02a77166b29a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 44cb89c86b7a48993b6987a3a40129782fd7a093

2:2b0a6af4b85e

    onlySigIsoforms = args$onlySigIsoforms,
    keepIsoformInAllConditions = args$keepIsoformInAllConditions2,
    showProgress = TRUE,
  )

  if (!is.null(args$stringtieAnnotation)) {
    SwitchList <- analyzeNovelIsoformORF(
      SwitchList,
      analysisAllIsoformsWithoutORF = TRUE,
      minORFlength = args$minORFlength,
      orfMethod = args$orfMethod,
      PTCDistance = args$PTCDistance,
      startCodons = "ATG",
      stopCodons = c("TAA", "TAG", "TGA"),
      showProgress = TRUE,
    )
  }

  ### Extract Sequences
  SwitchList <- extractSequence(
    SwitchList,
    onlySwitchingGenes = args$onlySwitchingGenes,

3:02a77166b29a

    onlySigIsoforms = args$onlySigIsoforms,
    keepIsoformInAllConditions = args$keepIsoformInAllConditions2,
    showProgress = TRUE,
  )

  # Analyze missing annotated isoforms by default
  SwitchList <- analyzeNovelIsoformORF(
    SwitchList,
    analysisAllIsoformsWithoutORF = TRUE,
    minORFlength = args$minORFlength,
    orfMethod = args$orfMethod,
    PTCDistance = args$PTCDistance,
    startCodons = "ATG",
    stopCodons = c("TAA", "TAG", "TGA"),
    showProgress = TRUE,
  )

  ### Extract Sequences
  SwitchList <- extractSequence(
    SwitchList,
    onlySwitchingGenes = args$onlySwitchingGenes,