# HG changeset patch
# User iuc
# Date 1747400251 0
# Node ID f4f7f632815d516eeaad6dd474e7eff8c2f1aaa5
# Parent c4ff13d2aab39062269bf88470192a3a9c81057f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit f79f470b3b2516fb908f5fc6fadc05c626c7f8dc
diff -r c4ff13d2aab3 -r f4f7f632815d macros.xml
--- a/macros.xml Thu Jun 29 10:40:07 2023 +0000
+++ b/macros.xml Fri May 16 12:57:31 2025 +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 c4ff13d2aab3 -r f4f7f632815d samtools_coverage.xml
--- a/samtools_coverage.xml Thu Jun 29 10:40:07 2023 +0000
+++ b/samtools_coverage.xml Fri May 16 12:57:31 2025 +0000
@@ -1,5 +1,5 @@
-
- computes the depth at each position or region
+
+ Produces a histogram or table of coverage per chromosome
macros.xml