# HG changeset patch
# User devteam
# Date 1414428162 14400
# Node ID 6ffa7e68dc1fdbc7f68f3a205c05b5dd80afc255
Uploaded initial tool definition.
diff -r 000000000000 -r 6ffa7e68dc1f samtools_bedcov.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_bedcov.xml Mon Oct 27 12:42:42 2014 -0400
@@ -0,0 +1,62 @@
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+ on BAM files
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+ samtools
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+ samtools --version | head -n 1 | awk '{ print $2 }'
+ "${output}"
+ ]]>
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+**What it does**
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+This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
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+Show read depth per BED region.
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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 6ffa7e68dc1f test-data/eboVir3.1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.1.bed Mon Oct 27 12:42:42 2014 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500
+eboVir3 1500 2000
+eboVir3 1500 3000
diff -r 000000000000 -r 6ffa7e68dc1f test-data/eboVir3.2.bam
Binary file test-data/eboVir3.2.bam has changed
diff -r 000000000000 -r 6ffa7e68dc1f test-data/eboVir3.2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.2.bed Mon Oct 27 12:42:42 2014 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500
+eboVir3 1500 2000
+eboVir3 1500 3000
diff -r 000000000000 -r 6ffa7e68dc1f test-data/eboVir3.bam
Binary file test-data/eboVir3.bam has changed
diff -r 000000000000 -r 6ffa7e68dc1f test-data/samtools_bedcov_out1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_bedcov_out1.tab Mon Oct 27 12:42:42 2014 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500 7919
+eboVir3 1500 2000 3009
+eboVir3 1500 3000 9986
diff -r 000000000000 -r 6ffa7e68dc1f test-data/samtools_bedcov_out2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_bedcov_out2.tab Mon Oct 27 12:42:42 2014 -0400
@@ -0,0 +1,3 @@
+eboVir3 500 1500 7919 2094
+eboVir3 1500 2000 3009 1064
+eboVir3 1500 3000 9986 3455
diff -r 000000000000 -r 6ffa7e68dc1f tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Oct 27 12:42:42 2014 -0400
@@ -0,0 +1,6 @@
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