Mercurial > repos > iuc > qualimap_bamqc
changeset 1:4a89c6f84425 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
| author | iuc |
|---|---|
| date | Tue, 29 Oct 2019 09:14:20 -0400 |
| parents | ac607906f10a |
| children | e7fd6754d093 |
| files | qualimap_bamqc.xml test-data/features.gtf |
| diffstat | 2 files changed, 14 insertions(+), 6 deletions(-) [+] |
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--- a/qualimap_bamqc.xml Thu Oct 10 17:42:04 2019 -0400 +++ b/qualimap_bamqc.xml Tue Oct 29 09:14:20 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@"> +<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy1"> <macros> <import>qualimap_macros.xml</import> </macros> @@ -21,11 +21,12 @@ ## from $out_dir. #set $per_base_coverage_target = $coverage_file - qualimap bamqc - -bam '$input1' -outdir results -outformat html - --collect-overlap-pairs #if str($stats_regions.region_select) == 'custom_regions': - -gff ${stats_regions.regions} + ## Have qualimap detect file format by suffix + ## since its autodetection is unreliable. + #set $regions_file = '.'.join(['regions', str($stats_regions.regions.ext)]) + ln -s '${stats_regions.regions}' ${regions_file} && + #if $stats_regions.outside_stats: #set $report_name = 'qualimapReportOutsideRegions' #set $summary_report = 'outside_results.txt' @@ -35,9 +36,15 @@ #if $per_base_coverage: #set $per_base_coverage_target = '/dev/null' #end if - ${stats_regions.outside_stats} #end if #end if + + qualimap bamqc + -bam '$input1' -outdir results -outformat html + --collect-overlap-pairs + #if str($stats_regions.region_select) == 'custom_regions': + -gff ${regions_file} ${stats_regions.outside_stats} + #end if #if $per_base_coverage: $per_base_coverage $per_base_coverage_target #end if
--- a/test-data/features.gtf Thu Oct 10 17:42:04 2019 -0400 +++ b/test-data/features.gtf Tue Oct 29 09:14:20 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";