# HG changeset patch
# User devteam
# Date 1429651313 14400
# Node ID 3735f950b2f5700df5f8efd1e1c7303109ec1a07
# Parent fe83e6f8e65e6e344c91c93a03aa29d2283a4048
Uploaded
diff -r fe83e6f8e65e -r 3735f950b2f5 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 21 17:21:53 2015 -0400
@@ -0,0 +1,70 @@
+
+
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+ samtools
+
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+
+
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+ @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 fe83e6f8e65e -r 3735f950b2f5 samtools_rmdup.xml
--- a/samtools_rmdup.xml Thu Mar 27 15:26:52 2014 -0400
+++ b/samtools_rmdup.xml Tue Apr 21 17:21:53 2015 -0400
@@ -1,8 +1,11 @@
-
-
- samtools
-
+remove PCR duplicates
+
+ macros.xml
+
+
+
+ samtools rmdup
#if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
${bam_paired_end_type.force_se}
@@ -10,18 +13,17 @@
-s
#end if
"$input1" "$output1"
- 2>&1 || echo "Error running samtools rmdup." >&2
-
+
-
+
-
+
@@ -32,38 +34,21 @@
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**What it does**
-This tool uses the SAMTools_ toolkit to remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).
-
-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
-------
+Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). This tool has the following parameters::
-**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.*
+ -s rmdup for SE reads
+ -S treat PE reads as SE in rmdup (force -s)
+
diff -r fe83e6f8e65e -r 3735f950b2f5 test-data/1.bam
Binary file test-data/1.bam has changed
diff -r fe83e6f8e65e -r 3735f950b2f5 test-data/samtools-rmdup-input1.bam
Binary file test-data/samtools-rmdup-input1.bam has changed
diff -r fe83e6f8e65e -r 3735f950b2f5 test-data/samtools-rmdup-test1.bam
Binary file test-data/samtools-rmdup-test1.bam has changed
diff -r fe83e6f8e65e -r 3735f950b2f5 tool_dependencies.xml
--- a/tool_dependencies.xml Thu Mar 27 15:26:52 2014 -0400
+++ b/tool_dependencies.xml Tue Apr 21 17:21:53 2015 -0400
@@ -1,6 +1,6 @@
-
-
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+