# HG changeset patch
# User devteam
# Date 1420821308 18000
# Node ID 76b2f1eee5084f9592a6bdc18b709d8db4ebfb56
Uploaded
diff -r 000000000000 -r 76b2f1eee508 bamtools.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools.xml Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,293 @@
+
+
+ BAM datasets and perform other transformations
+
+ bamtools
+ samtools
+
+
+
+ ##set up input files
+
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&
+ ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
+ #end for
+
+ #if str( $analysis_type.analysis_type_selector ) == "convert":
+ #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+ #set $reference_fasta_filename = "localref.fa"
+ #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
+ ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
+ samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
+ #else:
+ #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
+ #end if
+ #end if
+ #end if
+
+ ##finished setting up inputs
+
+ ##start bamtools commandline
+
+ bamtools
+
+ #if str( $analysis_type.analysis_type_selector ) == "convert":
+
+ convert
+
+ -format ${analysis_type.format_type.format_type_selector}
+
+ #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+
+ ${analysis_type.format_type.mapqual}
+ -fasta "${reference_fasta_filename}"
+
+ #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
+
+ ${analysis_type.format_type.noheader}
+
+ #end if
+
+ -out $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "count":
+
+ count
+ > $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "coverage":
+
+ coverage
+ -out $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "header":
+
+ header
+ > $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "merge":
+
+ merge
+ -out $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "random":
+
+ random
+ -n ${analysis_type.count}
+ -seed ${analysis_type.seed}
+ -out $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "revert":
+
+ revert
+ ${analysis_type.keepDuplicate}
+ ${analysis_type.keepQualities}
+ -out $out_file1
+
+ #elif str( $analysis_type.analysis_type_selector ) == "sort":
+
+ sort
+ ${analysis_type.byname}
+ -out $out_file1
+
+ #end if
+
+ #for $bam_count, $input_bam in enumerate( $input_bams ):
+ -in "localbam_${bam_count}.bam"
+ #end for
+
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+
+**What is does**
+
+BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
+This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.
+
+-----
+
+**Convert**
+
+Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either
+cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
+
+-----
+
+**Count**
+
+Counts a number of alignments in a BAM dataset(s).
+
+-----
+
+**Coverage**
+
+Prints per-base coverage for a BAM dataset.
+
+-----
+
+**Header**
+
+Prints header from a BAM dataset(s).
+
+------
+
+**Merge**
+
+Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button.
+
+------
+
+**Random**
+
+Grabs a specified number of random lines from BAM dataset(s).
+
+------
+
+**Revert**
+
+Removes duplicate marks and restores original (non-recalibrated) base qualities.
+
+-----
+
+.. class:: infomark
+
+**More information**
+
+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
+
+
+
+ 10.1093/bioinformatics/btr174
+
+
diff -r 000000000000 -r 76b2f1eee508 shed_upload.tar.gz
Binary file shed_upload.tar.gz has changed
diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-convert-pileup.pu
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools-convert-pileup.pu Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,239 @@
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diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-count.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools-count.tab Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,1 @@
+10
diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-coverage.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools-coverage.tab Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,4553 @@
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diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-fasta.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools-fasta.fa Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-header.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools-header.txt Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,3 @@
+@SQ SN:phiX174 LN:5386
+@PG ID:bwa PN:bwa VN:0.5.9-r16
+
diff -r 000000000000 -r 76b2f1eee508 test-data/bamtools-input1.bam
Binary file test-data/bamtools-input1.bam has changed
diff -r 000000000000 -r 76b2f1eee508 tool-data/sam_fa_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files. You will need
+#to create these data files and then create a sam_fa_indices.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The sam_fa_indices.loc
+#file has this format (white space characters are TAB characters):
+#
+#index
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/sam/,
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index hg18 /depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for
+#each index set you have stored. The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file. For example:
+#
+#index hg18 /depot/data2/galaxy/sam/hg18.fa
+#index hg19 /depot/data2/galaxy/sam/hg19.fa
diff -r 000000000000 -r 76b2f1eee508 tool-data/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,8 @@
+
+
+
+
+ line_type, value, path
+
+
+
diff -r 000000000000 -r 76b2f1eee508 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jan 09 11:35:08 2015 -0500
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+