Mercurial > repos > iuc > isoformswitchanalyzer
changeset 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 |
| files | IsoformSwitchAnalyzeR.R macros.xml |
| diffstat | 2 files changed, 12 insertions(+), 13 deletions(-) [+] |
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--- 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(
--- 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>