# HG changeset patch # User iuc # Date 1632841816 0 # Node ID 90f2dd176d806213052d12b090b15ed9159fcc02 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e" diff -r 000000000000 -r 90f2dd176d80 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 28 15:10:16 2021 +0000 @@ -0,0 +1,223 @@ + + + + samtools + + + + 1.13 + 20.05 + + + + + + + + + @HELP@ + + + + + + + + + + + + + + + + + + + + + + @HELP@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$ + + + + + + + + + + + + + @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},} + + + + + &1 | grep Version]]> + + + + + + + diff -r 000000000000 -r 90f2dd176d80 samtools_coverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_coverage.xml Tue Sep 28 15:10:16 2021 +0000 @@ -0,0 +1,126 @@ + + computes the depth at each position or region + + macros.xml + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + +
+ + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + = 1 +- coverage Proportion of covered bases [0..1] +- meandepth Mean depth of coverage +- meanbaseq Mean baseQ in covered region +- meanmapq Mean mapQ of selected reads + + ]]> + +
diff -r 000000000000 -r 90f2dd176d80 test-data/results_1.tabular diff -r 000000000000 -r 90f2dd176d80 test-data/results_2.txt diff -r 000000000000 -r 90f2dd176d80 test-data/results_3.txt diff -r 000000000000 -r 90f2dd176d80 test-data/test_1.bam Binary file test-data/test_1.bam has changed diff -r 000000000000 -r 90f2dd176d80 test-data/test_2.bam Binary file test-data/test_2.bam has changed