# HG changeset patch
# User devteam
# Date 1444755360 14400
# Node ID 191cec7b989b79f2d7da6964baa0affd9ff3a1ae
# Parent 346239545aa0f767e8d489c3c27fa14e7199753c
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 346239545aa0 -r 191cec7b989b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Oct 13 12:56:00 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 346239545aa0 -r 191cec7b989b samtools_sort.xml
--- a/samtools_sort.xml Thu Oct 16 12:42:20 2014 -0400
+++ b/samtools_sort.xml Tue Oct 13 12:56:00 2015 -0400
@@ -1,18 +1,17 @@
-
-
- samtools
-
- a BAM file
- samtools --version | head -n 1 | awk '{ print $2 }'
- samtools sort $sort_mode "${input1}" -o "${output1}" -O bam -T dataset
-
-
-
+
+ BAM dataset
+
+ macros.xml
+
+
+
+
+ samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"
-
+
@@ -23,22 +22,19 @@
+
+
+
+
+
**What it does**
-This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.
-
-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
-------
+This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
-**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 346239545aa0 -r 191cec7b989b test-data/1_sort_read_names.bam
Binary file test-data/1_sort_read_names.bam has changed
diff -r 346239545aa0 -r 191cec7b989b tool_dependencies.xml
--- a/tool_dependencies.xml Thu Oct 16 12:42:20 2014 -0400
+++ b/tool_dependencies.xml Tue Oct 13 12:56:00 2015 -0400
@@ -1,6 +1,6 @@
-
-
+
+