# HG changeset patch
# User devteam
# Date 1444755247 14400
# Node ID 4f7acd7af6173b0c7bc1e8380cfe1a98f879a65b
# Parent 6ffa7e68dc1fdbc7f68f3a205c05b5dd80afc255
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 6ffa7e68dc1f -r 4f7acd7af617 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Oct 13 12:54:07 2015 -0400
@@ -0,0 +1,70 @@
+
+
+
+ samtools
+
+
+
+
+
+
+ @misc{SAM_def,
+ title={Definition of SAM/BAM format},
+ url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+
+ 10.1093/bioinformatics/btp352
+ 10.1093/bioinformatics/btr076
+ 10.1093/bioinformatics/btr509
+
+ @misc{Danecek_et_al,
+ Author={Danecek, P., Schiffels, S., Durbin, R.},
+ title={Multiallelic calling model in bcftools (-m)},
+ url = {http://samtools.github.io/bcftools/call-m.pdf},}
+
+
+ @misc{Durbin_VCQC,
+ Author={Durbin, R.},
+ title={Segregation based metric for variant call QC},
+ url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+
+
+ @misc{Li_SamMath,
+ Author={Li, H.},
+ title={Mathematical Notes on SAMtools Algorithms},
+ url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+
+
+ @misc{SamTools_github,
+ title={SAMTools GitHub page},
+ url = {https://github.com/samtools/samtools},}
+
+
+
+
+ samtools --version | head -n 1 | awk '{ print $2 }'
+
+
+
+
+
+
+
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
+
+
+
+
diff -r 6ffa7e68dc1f -r 4f7acd7af617 samtools_bedcov.xml
--- a/samtools_bedcov.xml Mon Oct 27 12:42:42 2014 -0400
+++ b/samtools_bedcov.xml Tue Oct 13 12:54:07 2015 -0400
@@ -1,9 +1,11 @@
-
- on BAM files
-
- samtools
-
- samtools --version | head -n 1 | awk '{ print $2 }'
+
+ calculate read depth for a set of genomic intervals
+
+ macros.xml
+
+
+
+
"${output}"
- ]]>
-
-
-
+ ]]>
+
@@ -47,16 +47,11 @@
**What it does**
-This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
-
-Show read depth per BED region.
-
-**Citation**
+Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
-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>`_
-
+ samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
diff -r 6ffa7e68dc1f -r 4f7acd7af617 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Oct 27 12:42:42 2014 -0400
+++ b/tool_dependencies.xml Tue Oct 13 12:54:07 2015 -0400
@@ -1,6 +1,6 @@
-
-
+
+