# HG changeset patch
# User devteam
# Date 1444755260 14400
# Node ID 609810451a80f2d9d4421760a3631b1f17345423
# Parent 787d6c86c6eabe9ed9393106eca03b6314870fc0
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 787d6c86c6ea -r 609810451a80 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Oct 13 12:54:20 2015 -0400
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+ samtools
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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 }'
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+-----
+
+.. 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.
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diff -r 787d6c86c6ea -r 609810451a80 samtools_calmd.xml
--- a/samtools_calmd.xml Mon Sep 29 12:16:47 2014 -0400
+++ b/samtools_calmd.xml Tue Oct 13 12:54:20 2015 -0400
@@ -1,9 +1,11 @@
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- MD/NM tags and '=' bases
-
- samtools
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- samtools --version | head -n 1 | awk '{ print $2 }'
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+ recalculate MD/NM tags
+
+ macros.xml
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+
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+ "$calmd_output" ]]>
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@@ -46,10 +45,10 @@
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@@ -59,52 +58,42 @@
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**What it does**
-Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file.
+Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options::
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+ -e change identical bases to '='
+ -A modify the quality string
+ -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)
+ -E extended BAQ for better sensitivity but lower specificity
+
+-----
-**Citation**
+**NM and MD tags**
-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>`_
-
+From SAM format specification::
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+ MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
+ NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping
+
+See refernces for more information about SAM format tags.
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diff -r 787d6c86c6ea -r 609810451a80 tool-data/tool_data_table_conf.xml.sample
--- a/tool-data/tool_data_table_conf.xml.sample Mon Sep 29 12:16:47 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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