# HG changeset patch
# User devteam
# Date 1444755332 14400
# Node ID b1b3677920346da3032f1ebc115177a2a57d7003
# Parent 75e4b89f100435e88ebb0275432baff038348fbe
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 75e4b89f1004 -r b1b367792034 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Oct 13 12:55:32 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 75e4b89f1004 -r b1b367792034 samtools_rmdup.xml
--- a/samtools_rmdup.xml Thu Mar 27 14:05:46 2014 -0400
+++ b/samtools_rmdup.xml Tue Oct 13 12:55:32 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 75e4b89f1004 -r b1b367792034 test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 75e4b89f1004 -r b1b367792034 test-data/samtools-rmdup-input1.bam
Binary file test-data/samtools-rmdup-input1.bam has changed
diff -r 75e4b89f1004 -r b1b367792034 test-data/samtools-rmdup-test1.bam
Binary file test-data/samtools-rmdup-test1.bam has changed
diff -r 75e4b89f1004 -r b1b367792034 tool_dependencies.xml
--- a/tool_dependencies.xml Thu Mar 27 14:05:46 2014 -0400
+++ b/tool_dependencies.xml Tue Oct 13 12:55:32 2015 -0400
@@ -1,6 +1,6 @@
-
-
+
+