# HG changeset patch
# User devteam
# Date 1377541371 14400
# Node ID 13c4ad597626d8bbbe07920f3d08cb7fc36c35a5
Uploaded tool tarball.
diff -r 000000000000 -r 13c4ad597626 samtools_flagstat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_flagstat.xml Mon Aug 26 14:22:51 2013 -0400
@@ -0,0 +1,37 @@
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+ samtools
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+ provides simple stats on BAM files
+ samtools flagstat "$input1" > "$output1"
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+**What it does**
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+This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
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+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+
+------
+
+**Citation**
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+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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diff -r 000000000000 -r 13c4ad597626 test-data/3unsorted.bam
Binary file test-data/3unsorted.bam has changed
diff -r 000000000000 -r 13c4ad597626 test-data/samtools_flagstat_out1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_flagstat_out1.txt Mon Aug 26 14:22:51 2013 -0400
@@ -0,0 +1,11 @@
+10 + 0 in total (QC-passed reads + QC-failed reads)
+0 + 0 duplicates
+10 + 0 mapped (100.00%:nan%)
+0 + 0 paired in sequencing
+0 + 0 read1
+0 + 0 read2
+0 + 0 properly paired (nan%:nan%)
+0 + 0 with itself and mate mapped
+0 + 0 singletons (nan%:nan%)
+0 + 0 with mate mapped to a different chr
+0 + 0 with mate mapped to a different chr (mapQ>=5)
diff -r 000000000000 -r 13c4ad597626 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Aug 26 14:22:51 2013 -0400
@@ -0,0 +1,6 @@
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