# 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 @@
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+ samtools
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+ 1.13
+ 20.05
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+ @HELP@
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+ @HELP@
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+ ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$
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+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/},}
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+ 10.1093/bioinformatics/btp352
+ 10.1093/bioinformatics/btr076
+ 10.1093/bioinformatics/btr509
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+ @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},}
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+ @misc{Durbin_VCQC,
+ Author={Durbin, R.},
+ title={Segregation based metric for variant call QC},
+ url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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+ @misc{Li_SamMath,
+ Author={Li, H.},
+ title={Mathematical Notes on SAMtools Algorithms},
+ url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
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+ &1 | grep Version]]>
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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 @@
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+ computes the depth at each position or region
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+ macros.xml
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+ = 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
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+ ]]>
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+
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