# HG changeset patch # User martenson # Date 1410405134 14400 # Node ID 5e12c7427fa34d38712ee45e958786f8080f6f08 # Parent 5c01430e6e76e8ca818971a31b6d56593096991d new initial commit diff -r 5c01430e6e76 -r 5e12c7427fa3 samtools_sort.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_sort.xml Wed Sep 10 23:12:14 2014 -0400 @@ -0,0 +1,47 @@ + + + samtools + + a BAM file + + samtools sort + $sort_mode + "${input1}" foo + 2>&1 || echo "Error running samtools sort." >&2 + ; + mv foo.bam "${output1}" + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + +------ + +**Citation** + +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>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + + diff -r 5c01430e6e76 -r 5e12c7427fa3 test-data/1.bam Binary file test-data/1.bam has changed diff -r 5c01430e6e76 -r 5e12c7427fa3 test-data/1_sort.bam Binary file test-data/1_sort.bam has changed diff -r 5c01430e6e76 -r 5e12c7427fa3 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 10 23:12:14 2014 -0400 @@ -0,0 +1,6 @@ + + + + + +