# HG changeset patch
# User iuc
# Date 1684935233 0
# Node ID 02a77166b29a976534848c3f0a9859d0793c45b5
# Parent  2b0a6af4b85ef3bf9eadfc0ecd4550041ceb99b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 44cb89c86b7a48993b6987a3a40129782fd7a093

diff -r 2b0a6af4b85e -r 02a77166b29a IsoformSwitchAnalyzeR.R
--- 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(
diff -r 2b0a6af4b85e -r 02a77166b29a macros.xml
--- a/macros.xml	Wed May 24 06:06:54 2023 +0000
+++ b/macros.xml	Wed May 24 13:33:53 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.20.0</token>
-    <token name="@SUFFIX_VERSION@">2</token>
+    <token name="@SUFFIX_VERSION@">3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement>