# HG changeset patch # User devteam # Date 1394643210 14400 # Node ID 3aa48bcbc599131965aae30196eea3ed3ecbd616 # Parent b47a418ccfdc9a4ed8a26b7054789b00313f34d6 Uploaded tarball for 0.0.3 version. diff -r b47a418ccfdc -r 3aa48bcbc599 samtools_mpileup.xml --- a/samtools_mpileup.xml Wed Mar 12 12:52:52 2014 -0400 +++ b/samtools_mpileup.xml Wed Mar 12 12:53:30 2014 -0400 @@ -1,30 +1,46 @@ - - SNP and indel caller - - samtools - - samtools_wrapper.py - -p 'samtools mpileup' - --stdout "${output_log}" + + SNP and indel caller + + samtools + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + > "$output_mpileup" 2> "$output_log" + ]]> + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#set pasted_data = '' +#if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": + #set regex=re.compile("\\s+") + #set pasted_data = '\t'.join( regex.split( str( $advanced_options.exclude_read_group['read_groups'] ) ) ) + #end if +#end if +${pasted_data} +]]> + + + +#set pasted_data = '' +#if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": + #set regex=re.compile("\\s+") + #set pasted_data = '\t'.join( regex.split( str( $advanced_options.limit_by_region['region_paste'] ) ) ) + #end if +#end if +${pasted_data} +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** Generate BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. ------ -**Settings**:: +.. list-table:: **Input options** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -6 + - *BOOLEAN* + - assume the quality is in the Illumina-1.3+ encoding + - off + * - -A + - *BOOLEAN* + - count anomalous read pairs + - off + * - -B + - *BOOLEAN* + - disable BAQ computation + - off + * - -b + - *FILE* + - list of input BAM filenames, one per line + - *null* + * - -C + - *INT* + - parameter for adjusting mapQ; 0 to disable + - 0 + * - -d + - *INT* + - max per-BAM depth to avoid excessive memory usage + - 250 + * - -E + - *BOOLEAN* + - recalculate extended BAQ on the fly thus ignoring existing BQs + - off + * - -f + - *FILE* + - faidx indexed reference sequence file + - *null* + * - -G + - *FILE* + - exclude read groups listed in FILE + - *null* + * - -l + - *FILE* + - list of positions (chr pos) or regions (BED) + - *null* + * - -M + - *INT* + - cap mapping quality at INT + - 60 + * - -r + - *STR* + - region in which pileup is generated + - *null* + * - -R + - *BOOLEAN* + - ignore RG tags + - off + * - -q + - *INT* + - skip alignments with mapQ smaller than INT + - 0 + * - -Q + - *INT* + - skip bases with baseQ/BAQ smaller than INT + - 13 + * - --rf + - *INT* + - required flags: skip reads with mask bits unset + - 0 + * - --ff + - *INT* + - filter flags: skip reads with mask bits set + - 0 + +------ - Input Options: - -6 Assume the quality is in the Illumina 1.3+ encoding. - -A Do not skip anomalous read pairs in variant calling. - -B Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. - -b FILE List of input BAM files, one file per line [null] - -C INT Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. [0] - -d INT At a position, read maximally INT reads per input BAM. [250] - -E Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit. - -f FILE The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null] - -l FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null] - -q INT Minimum mapping quality for an alignment to be used [0] - -Q INT Minimum base quality for a base to be considered [13] - -r STR Only generate pileup in region STR [all sites] - Output Options: - - -D Output per-sample read depth - -g Compute genotype likelihoods and output them in the binary call format (BCF). - -S Output per-sample Phred-scaled strand bias P-value - -u Similar to -g except that the output is uncompressed BCF, which is preferred for piping. - - Options for Genotype Likelihood Computation (for -g or -u): - - -e INT Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20] - -h INT Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. [100] - -I Do not perform INDEL calling - -L INT Skip INDEL calling if the average per-sample depth is above INT. [250] - -o INT Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. [40] - -P STR Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA. [all] +.. list-table:: **Output options** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -D + - *BOOLEAN* + - output per-sample DP in BCF (require -g/-u) + - off + * - -g + - *BOOLEAN* + - generate BCF output (genotype likelihoods) + - off + * - -O + - *BOOLEAN* + - output base positions on reads (disabled by -g/-u) + - off + * - -s + - *BOOLEAN* + - output mapping quality (disabled by -g/-u) + - off + * - -S + - *BOOLEAN* + - output per-sample strand bias P-value in BCF (require -g/-u) + - off + * - -u + - *BOOLEAN* + - generate uncompressed BCF output + - off + +------ + +.. list-table:: **SNP/INDEL genotype likelihoods options (effective with '-g' or '-u')** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -e + - *INT* + - Phred-scaled gap extension seq error probability + - 20 + * - -F + - *FLOAT* + - minimum fraction of gapped reads for candidates + - 0.002 + * - -h + - *INT* + - coefficient for homopolymer errors + - 100 + * - -I + - *BOOLEAN* + - do not perform indel calling + - off + * - -L + - *INT* + - max per-sample depth for INDEL calling + - 250 + * - -m + - *INT* + - minimum gapped reads for indel candidates + - 1 + * - -o + - *INT* + - Phred-scaled gap open sequencing error probability + - 40 + * - -p + - *BOOLEAN* + - apply -m and -F per-sample to increase sensitivity + - off + * - -P + - *STR* + - comma separated list of platforms for indels + - all ------ @@ -207,7 +495,7 @@ 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.* - - - + + \ No newline at end of file diff -r b47a418ccfdc -r 3aa48bcbc599 samtools_wrapper.py --- a/samtools_wrapper.py Wed Mar 12 12:52:52 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -#!/usr/bin/env python -#Dan Blankenberg - -""" -A wrapper script for running SAMTools commands. -""" - -import sys, optparse, os, tempfile, subprocess, shutil -from string import Template - -GALAXY_EXT_TO_SAMTOOLS_EXT = { 'bam_index':'bam.bai', } #items not listed here will use the galaxy extension as-is -GALAXY_EXT_TO_SAMTOOLS_FILE_TYPE = GALAXY_EXT_TO_SAMTOOLS_EXT #for now, these are the same, but could be different if needed -DEFAULT_SAMTOOLS_PREFIX = "SAMTools_file" -CHUNK_SIZE = 2**20 #1mb - - -def cleanup_before_exit( tmp_dir ): - if tmp_dir and os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - -def SAMTOOLS_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ): - suffix = GALAXY_EXT_TO_SAMTOOLS_EXT.get( galaxy_ext, galaxy_ext ) - if prefix is None: - prefix = DEFAULT_SAMTOOLS_PREFIX - if target_dir is None: - target_dir = os.getcwd() - SAMTools_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) ) - os.symlink( galaxy_filename, SAMTools_filename ) - return SAMTools_filename - -def SAMTOOLS_filetype_argument_substitution( argument, galaxy_ext ): - return argument % dict( file_type = GALAXY_EXT_TO_SAMTOOLS_FILE_TYPE.get( galaxy_ext, galaxy_ext ) ) - -def open_file_from_option( filename, mode = 'rb' ): - if filename: - return open( filename, mode = mode ) - return None - -def html_report_from_directory( html_out, dir ): - html_out.write( '\n\nGalaxy - SAMTOOLS Output\n\n\n

\n

\n\n\n' ) - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to SAMTOOLS, without any modification.' ) - parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' ) - parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' ) - parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) - parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"') - (options, args) = parser.parse_args() - - tmp_dir = tempfile.mkdtemp( prefix='tmp-SAMTOOLS-' ) - - #set up stdout and stderr output options - stdout = open_file_from_option( options.stdout, mode = 'wb' ) - stderr = open_file_from_option( options.stderr, mode = 'wb' ) - #if no stderr file is specified, we'll use our own - if stderr is None: - stderr = tempfile.NamedTemporaryFile( prefix="SAMTOOLS-stderr-", dir=tmp_dir ) - - if options.pass_through_options: - cmd = ' '.join( options.pass_through_options ) - else: - cmd = '' - return_code = None - if options.datasets: - for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets: - SAMTools_filename = SAMTOOLS_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix ) - if dataset_arg: - if '>' in cmd: - cmd = cmd.replace( '>', ' %s "%s" >' % ( SAMTOOLS_filetype_argument_substitution( dataset_arg, galaxy_ext ), SAMTools_filename ), 1 ) - else: - cmd = '%s %s "%s"' % ( cmd, SAMTOOLS_filetype_argument_substitution( dataset_arg, galaxy_ext ), SAMTools_filename ) - #auto index fasta files: - if galaxy_ext == 'fa': - index_cmd = 'samtools faidx %s' % ( SAMTools_filename ) - proc = subprocess.Popen( args=index_cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) - return_code = proc.wait() - if return_code: - break - if return_code is None or not return_code: - proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) - return_code = proc.wait() - if return_code: - stderr_target = sys.stderr - else: - if stdout: - stderr_target = stdout - else: - stderr_target = sys.stdout - stderr.flush() - stderr.seek(0) - while True: - chunk = stderr.read( CHUNK_SIZE ) - if chunk: - stderr_target.write( chunk ) - else: - break - stderr.close() - #generate html reports - if options.html_report_from_directory: - for ( html_filename, html_dir ) in options.html_report_from_directory: - html_report_from_directory( open( html_filename, 'wb' ), html_dir ) - - cleanup_before_exit( tmp_dir ) - -if __name__=="__main__": __main__() diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam Binary file test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam has changed diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools/mpileup/samtools_mpileup_out_1.log --- a/test-data/samtools/mpileup/samtools_mpileup_out_1.log Wed Mar 12 12:52:52 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -[mpileup] 1 samples in 1 input files - Set max per-file depth to 8000 diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools/mpileup/samtools_mpileup_out_1.pileup --- a/test-data/samtools/mpileup/samtools_mpileup_out_1.pileup Wed Mar 12 12:52:52 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -phiX174 1411 A 1 ^P. $ -phiX174 1412 G 3 .^D.^F. "$$ -phiX174 1413 C 5 ...^D.^F. """$$ -phiX174 1414 G 6 .....^F. #####$ -phiX174 1415 C 7 ......^F. %%%%%%& -phiX174 1416 C 8 .......^F. $$$$$$$$ -phiX174 1417 G 9 ........^F. "#######$ -phiX174 1418 T 10 .........^F. """""""""$ -phiX174 1419 G 10 .......... """""'&'%$ -phiX174 1420 G 10 .......... """""""""" -phiX174 1421 A 10 .......... """""""""" -phiX174 1422 T 10 .......... """""""""" -phiX174 1423 G 10 .......... """""""""# -phiX174 1424 C 10 ..A.AAAAAA %""""""""" -phiX174 1425 C 10 .......... $$$""""""" -phiX174 1426 T 10 .......... #####""""" -phiX174 1427 G 10 .......... ######"""" -phiX174 1428 A 10 .......... """""""""" -phiX174 1429 C 10 .......... ((((((&("" -phiX174 1430 C 10 .......... $$$$$$$$$" -phiX174 1431 G 10 .......... ########## -phiX174 1432 T 10 .......... """""""""" -phiX174 1433 A 10 .......... ########## -phiX174 1434 C 10 .......... ((((((&(%$ -phiX174 1435 C 10 .......... $$$$$$$$$$ -phiX174 1436 G 10 .......... ########## -phiX174 1437 A 10 .......... 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"! -phiX174 1453 G 1 .$ ! diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools/mpileup/samtools_mpileup_out_2.bcf Binary file test-data/samtools/mpileup/samtools_mpileup_out_2.bcf has changed diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_in_1.bam Binary file test-data/samtools_mpileup_in_1.bam has changed diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_in_3.bam Binary file test-data/samtools_mpileup_in_3.bam has changed diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_1.log Wed Mar 12 12:53:30 2014 -0400 @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files + Set max per-file depth to 8000 diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_1.pileup Wed Mar 12 12:53:30 2014 -0400 @@ -0,0 +1,43 @@ +phiX174 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36,35,36,35,34,33,32,31 +phiX174 1449 A 0 DFFFFF 36,36,35,34,33,32 +phiX174 1450 T 0 FFFF 36,35,34,33 +phiX174 1451 G 0 FFF 36,35,34 +phiX174 1452 A 0 FF 36,35 +phiX174 1453 G 0 F 36 diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_2.bcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_2.bcf Wed Mar 12 12:53:30 2014 -0400 @@ -0,0 +1,33 @@ +##fileformat=VCFv4.1 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_2.log Wed Mar 12 12:53:30 2014 -0400 @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files + Set max per-file depth to 8000 diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_3.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_3.log Wed Mar 12 12:53:30 2014 -0400 @@ -0,0 +1,2 @@ +[mpileup] 1 samples in 1 input files + Set max per-file depth to 8000 diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_4.bcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_4.bcf Wed Mar 12 12:53:30 2014 -0400 @@ -0,0 +1,33 @@ +##fileformat=VCFv4.1 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT diff -r b47a418ccfdc -r 3aa48bcbc599 test-data/samtools_mpileup_out_4.log Binary file test-data/samtools_mpileup_out_4.log has changed diff -r b47a418ccfdc -r 3aa48bcbc599 tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample Wed Mar 12 12:52:52 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -#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 b47a418ccfdc -r 3aa48bcbc599 tool-data/tool_data_table_conf.xml.sample --- a/tool-data/tool_data_table_conf.xml.sample Wed Mar 12 12:52:52 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - - - - - line_type, value, path - -
- \ No newline at end of file diff -r b47a418ccfdc -r 3aa48bcbc599 tool_dependencies.xml --- a/tool_dependencies.xml Wed Mar 12 12:52:52 2014 -0400 +++ b/tool_dependencies.xml Wed Mar 12 12:53:30 2014 -0400 @@ -1,6 +1,6 @@ - - + +