# HG changeset patch
# User iuc
# Date 1403276077 14400
# Node ID 80fffde691eb71dac1e88d7216cda2b48e1fd221
Uploaded
diff -r 000000000000 -r 80fffde691eb samtools_sort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_sort.xml Fri Jun 20 10:54:37 2014 -0400
@@ -0,0 +1,45 @@
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+ samtools
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+ a BAM file
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+ samtools sort
+ $sort_mode
+ "${input1}" "${output1}"
+ 2>&1 || echo "Error running samtools sort." >&2
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+**What it does**
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+This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.
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+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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+------
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+**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 80fffde691eb test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 000000000000 -r 80fffde691eb tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jun 20 10:54:37 2014 -0400
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