Mercurial > repos > iuc > qualimap_rnaseq
changeset 1:ce0da6c9f49e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
| author | iuc |
|---|---|
| date | Tue, 29 Oct 2019 09:14:03 -0400 |
| parents | 613e6446ea5d |
| children | 43a1c3e1a4d0 |
| files | qualimap_rnaseq.xml test-data/features.gtf |
| diffstat | 2 files changed, 7 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/qualimap_rnaseq.xml Thu Oct 10 17:41:10 2019 -0400 +++ b/qualimap_rnaseq.xml Tue Oct 29 09:14:03 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@"> +<tool id="qualimap_rnaseq" name="QualiMap RNA-Seq QC" version="@VERSION@+galaxy1"> <macros> <import>qualimap_macros.xml</import> </macros> @@ -7,9 +7,13 @@ <command detect_errors="exit_code"><![CDATA[ @SET_JAVA_OPTS@ && + ## Have qualimap detect file format by suffix + ## since its autodetection is unreliable. + ln -s '$features' features.gtf && + qualimap rnaseq -bam '${seq_info.input}' - -gtf '$features' + -gtf features.gtf ${seq_info.treat_as_pe} ${seq_info.sorted} ${counts_out.report_counts}
--- a/test-data/features.gtf Thu Oct 10 17:41:10 2019 -0400 +++ b/test-data/features.gtf Tue Oct 29 09:14:03 2019 -0400 @@ -1,3 +1,4 @@ +#comment lines (like this one) break qualimap's regions file autodetection test_chromosome test gene 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; test_chromosome test transcript 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; test_chromosome test exon 1 300 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";