# 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 @@ + + on BAM files + + samtools + + samtools --version | head -n 1 | awk '{ print $2 }' + "${output}" + ]]> + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool runs the ``samtools bedcov`` command in the SAMtools toolkit. + +Show read depth per BED region. + +**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 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 @@ + + + + + +