Mercurial > repos > ebi-gxa > gtf2gene_list
changeset 5:00ee933b08fd draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 2d7ec5b8aa6d292cbb4a1b60efd1d98ff23263ba
| author | ebi-gxa |
|---|---|
| date | Fri, 01 Nov 2019 09:44:26 -0400 |
| parents | b6354c917ef9 |
| children | 1a642de6db01 |
| files | gtf2featureAnnotation.R gtf2featureAnnotation.xml |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- 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
--- 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>