# HG changeset patch
# User ebi-gxa
# Date 1572615866 14400
# Node ID 00ee933b08fd50e3f4bdb1db3a2bdc72cd2f6b13
# Parent  b6354c917ef9a73f28be3225ea30e7aa52f69126
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 2d7ec5b8aa6d292cbb4a1b60efd1d98ff23263ba

diff -r b6354c917ef9 -r 00ee933b08fd gtf2featureAnnotation.R
--- a/gtf2featureAnnotation.R	Fri Oct 25 09:25:20 2019 -0400
+++ b/gtf2featureAnnotation.R	Fri Nov 01 09:44:26 2019 -0400
@@ -154,7 +154,8 @@
 # Version transcripts
 
 if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){
-  anno$transcript_id <- paste(anno$transcript_id, anno$transcript_version, sep='.')
+  has_transcript_version <- ! is.na(anno$transcript_version)
+  anno$transcript_id[has_transcript_version] <- paste(anno$transcript_id[has_transcript_version], anno$transcript_version[has_transcript_version], sep='.')
 }
 
 # If specified, filter down a provided cDNA FASTA file
diff -r b6354c917ef9 -r 00ee933b08fd gtf2featureAnnotation.xml
--- a/gtf2featureAnnotation.xml	Fri Oct 25 09:25:20 2019 -0400
+++ b/gtf2featureAnnotation.xml	Fri Nov 01 09:44:26 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy4">
+<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy5">
     <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
     <requirements>
       <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>