# HG changeset patch
# User devteam
# Date 1429652478 14400
# Node ID a430da4f04cdf8e85868711bbebd72bd255d84fe
Uploaded
diff -r 000000000000 -r a430da4f04cd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 21 17:41:18 2015 -0400
@@ -0,0 +1,70 @@
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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},}
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+
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+
+ 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 000000000000 -r a430da4f04cd samtools_sort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_sort.xml Tue Apr 21 17:41:18 2015 -0400
@@ -0,0 +1,40 @@
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+ BAM dataset
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+ macros.xml
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+ samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"
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+**What it does**
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+This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
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diff -r 000000000000 -r a430da4f04cd test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 000000000000 -r a430da4f04cd test-data/1_sort.bam
Binary file test-data/1_sort.bam has changed
diff -r 000000000000 -r a430da4f04cd test-data/1_sort_read_names.bam
Binary file test-data/1_sort_read_names.bam has changed
diff -r 000000000000 -r a430da4f04cd tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Apr 21 17:41:18 2015 -0400
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