Mercurial > repos > iuc > isoformswitchanalyzer

diff IsoformSwitchAnalyzeR.R @ 3:02a77166b29a draft

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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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line diff
--- a/IsoformSwitchAnalyzeR.R	Wed May 24 06:06:54 2023 +0000
+++ b/IsoformSwitchAnalyzeR.R	Wed May 24 13:33:53 2023 +0000
@@ -514,18 +514,17 @@
     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,
-    )
-  }
+  # 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(