# 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