# HG changeset patch
# User devteam
# Date 1444755305 14400
# Node ID c21cb56fbbbcb307ab8b2ec6f91285342378fe9a
# Parent 2656247b52532a39e8681ab356eddd173d2ba7fb
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 2656247b5253 -r c21cb56fbbbc macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Oct 13 12:55:05 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 $2 }'
+
+
+
+
+
+
+
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
+
+
+
+
diff -r 2656247b5253 -r c21cb56fbbbc samtools_phase.xml
--- a/samtools_phase.xml Fri Sep 26 15:20:35 2014 -0400
+++ b/samtools_phase.xml Tue Oct 13 12:55:05 2015 -0400
@@ -1,8 +1,11 @@
-
+
heterozygous SNPs
-
- samtools
-
+
+ macros.xml
+
+
+
+
samtools phase -b "phase_wrapper"
#if str($option_set.option_sets) == 'advanced':
${option_set.ignore_chimeras}
@@ -16,9 +19,6 @@
#end if
"$input_bam" > "$phase_sets"
-
-
-
@@ -125,14 +125,6 @@
- Drop reads with ambiguous phase
- *off*
-------
-
-**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 2656247b5253 -r c21cb56fbbbc tool_dependencies.xml
--- a/tool_dependencies.xml Fri Sep 26 15:20:35 2014 -0400
+++ b/tool_dependencies.xml Tue Oct 13 12:55:05 2015 -0400
@@ -1,6 +1,6 @@
-
-
+
+