# HG changeset patch # User iuc # Date 1725765691 0 # Node ID b5386f2f01e76e968a268c8c223cf5527e623f17 # Parent 6c790feb4215f78dcd5fed6fddd76a9520d7bfb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c diff -r 6c790feb4215 -r b5386f2f01e7 macros.xml --- a/macros.xml Mon Aug 15 09:06:00 2022 +0000 +++ b/macros.xml Sun Sep 08 03:21:31 2024 +0000 @@ -5,8 +5,15 @@ - 1.15.1 - 20.05 + + 1.20 + 2 + 22.05 - - @misc{SAM_def, - title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/},} - - 10.1093/bioinformatics/btp352 - 10.1093/bioinformatics/btr076 - 10.1093/bioinformatics/btr509 - - @misc{Danecek_et_al, - Author={Danecek, P., Schiffels, S., Durbin, R.}, - title={Multiallelic calling model in bcftools (-m)}, - url = {http://samtools.github.io/bcftools/call-m.pdf},} - - - @misc{Durbin_VCQC, - Author={Durbin, R.}, - title={Segregation based metric for variant call QC}, - url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} - - - @misc{Li_SamMath, - Author={Li, H.}, - title={Mathematical Notes on SAMtools Algorithms}, - url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} - - - @misc{SamTools_github, - title={SAMTools GitHub page}, - url = {https://github.com/samtools/samtools},} - + 10.1093/gigascience/giab008 diff -r 6c790feb4215 -r b5386f2f01e7 samtools_bam_to_cram.xml --- a/samtools_bam_to_cram.xml Mon Aug 15 09:06:00 2022 +0000 +++ b/samtools_bam_to_cram.xml Sun Sep 08 03:21:31 2024 +0000 @@ -1,4 +1,4 @@ - + convert BAM alignments to CRAM format diff -r 6c790feb4215 -r b5386f2f01e7 test-data/test2.cram Binary file test-data/test2.cram has changed diff -r 6c790feb4215 -r b5386f2f01e7 test-data/test_bam.cram Binary file test-data/test_bam.cram has changed diff -r 6c790feb4215 -r b5386f2f01e7 test-data/test_chr1.cram Binary file test-data/test_chr1.cram has changed diff -r 6c790feb4215 -r b5386f2f01e7 test-data/test_regions.cram Binary file test-data/test_regions.cram has changed diff -r 6c790feb4215 -r b5386f2f01e7 test-data/test_sam.cram Binary file test-data/test_sam.cram has changed