| Previous changeset 3:973fea5b4bdf (2014-03-27) Next changeset 5:aa0ef6f0ee89 (2015-05-08) |
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Commit message:
Uploaded |
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modified:
samtools_mpileup.xml tool_dependencies.xml |
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added:
macros.xml test-data/phiX.bam test-data/phiX_1.bam test-data/samtools_mpileup_in_1.bam test-data/samtools_mpileup_out_1.log test-data/samtools_mpileup_out_1.pileup test-data/samtools_mpileup_out_2.log test-data/samtools_mpileup_out_2.vcf test-data/samtools_mpileup_out_3.log test-data/samtools_mpileup_out_4.log test-data/samtools_mpileup_out_4.vcf |
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removed:
samtools_wrapper.py test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 21 16:29:10 2015 -0400 |
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| @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @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},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros> |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 samtools_mpileup.xml --- a/samtools_mpileup.xml Thu Mar 27 15:27:36 2014 -0400 +++ b/samtools_mpileup.xml Tue Apr 21 16:29:10 2015 -0400 |
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| b'@@ -1,213 +1,371 @@\n-<tool id="samtools_mpileup" name="MPileup" version="0.0.3">\n- <description>SNP and indel caller</description>\n- <requirements>\n- <requirement type="package" version="0.1.19">samtools</requirement>\n- </requirements>\n- <command interpreter="python">samtools_wrapper.py\n- -p \'samtools mpileup\'\n- --stdout "${output_log}"\n+<tool id="samtools_mpileup" name="MPileup" version="2.0">\n+ <description>call variants</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" />\n+ <command>\n+ <![CDATA[\n+ #if $reference_source.reference_source_selector == "history":\n+ ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup\n+ #else:\n+ samtools mpileup\n+ #end if\n #if $reference_source.reference_source_selector != "history":\n- -p \'-f "${reference_source.ref_file.fields.path}"\'\n+ -f "${reference_source.ref_file.fields.path}"\n #else:\n- -d "-f" "${reference_source.ref_file}" "fa" "reference_input"\n+ -f "${reference_source.ref_file}"\n #end if\n #for $i, $input_bam in enumerate( $reference_source.input_bams ):\n- -d " " "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "bam_input_${i}"\n- -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "bam_input_${i}" ##hardcode galaxy ext type as bam_index\n+ "${input_bam.input_bam}"\n #end for\n- -p \'\n #if str( $advanced_options.advanced_options_selector ) == "advanced":\n- ${advanced_options.skip_anomalous_read_pairs}\n+ #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":\n+ #if $advanced_options.filter_by_flags.require_flags:\n+ --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(\',\')])}\n+ #end if\n+ #if $advanced_options.filter_by_flags.exclude_flags:\n+ --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(\',\')])}\n+ #end if\n+ #end if\n+ #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":\n+ -l "$pasted_regions"\n+ #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"\n+ -l "$bed_regions"\n+ #end if\n+ #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":\n+ -G "$excluded_read_groups"\n+ #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"\n+ -G "$read_groups"\n+ #end if\n+ ${advanced_options.skip_anomalous_read_pairs}\n ${advanced_options.disable_probabilistic_realignment}\n -C "${advanced_options.coefficient_for_downgrading}"\n -d "${advanced_options.max_reads_per_bam}"\n ${advanced_options.extended_BAQ_computation}\n- #if str( $advanced_options.position_list ) != \'None\':\n- -l "${advanced_options.position_list}"\n- #end if\n -q "${advanced_options.minimum_mapping_quality}"\n -Q "${advanced_options.minimum_base_quality}"\n #if str( $advanced_options.region_string ):\n -r "${advanced_options.region_string}"\n #end if\n- ${advanced_options.output_per_sample_read_depth}\n- ${advanced_options.output_per_sample_strand_bias_p_value}\n+ \n #end if\n #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == \'perform_genotype_likelihood_computation\':\n- ##-g or -u\n- -g\n- -e "${genotype_likelihood_computation_type.gap_extension_sequencing_error_probability}"\n- -h "${genotype_likelihood_computation_type.coefficient_for_modeling_homopolymer_errors}"\n+ ##\n+\n+ ${genotype_likelihood_computation_type.output_format}\n+ ${genotype'..b'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]\n- -d INT \tAt a position, read maximally INT reads per input BAM. [250]\n- -E \tExtended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit.\n- -f FILE \tThe faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null]\n- -l FILE \tBED or position list file containing a list of regions or sites where pileup or BCF should be generated [null]\n- -q INT \tMinimum mapping quality for an alignment to be used [0]\n- -Q INT \tMinimum base quality for a base to be considered [13]\n- -r STR \tOnly generate pileup in region STR [all sites]\n- Output Options:\n- \t\n- -D \tOutput per-sample read depth\n- -g \tCompute genotype likelihoods and output them in the binary call format (BCF).\n- -S \tOutput per-sample Phred-scaled strand bias P-value\n- -u \tSimilar to -g except that the output is uncompressed BCF, which is preferred for piping.\n- \n- Options for Genotype Likelihood Computation (for -g or -u):\n- \t\n- -e INT \tPhred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20]\n- -h INT \tCoefficient 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]\n- -I \tDo not perform INDEL calling\n- -L INT \tSkip INDEL calling if the average per-sample depth is above INT. [250]\n- -o INT \tPhred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. [40]\n- -P STR \tComma 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]\n+ -e, --ext-prob INT Phred-scaled gap extension seq error probability [20]\n+ -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002]\n+ -h, --tandem-qual INT coefficient for homopolymer errors [100]\n+ -I, --skip-indels do not perform indel calling\n+ -L, --max-idepth INT maximum per-sample depth for INDEL calling [250]\n+ -m, --min-ireads INT minimum number gapped reads for indel candidates [1]\n+ -o, --open-prob INT Phred-scaled gap open seq error probability [40]\n+ -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity\n+ -P, --platforms STR comma separated list of platforms for indels [all]\n \n-------\n-\n-**Citation**\n-\n-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>`_\n-\n-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n-\n- </help>\n+**Notes**: Assuming diploid individuals.\n+]]>\n+ </help>\n+ <configfiles>\n+ <configfile name="excluded_read_groups">\n+<![CDATA[\n+#set pasted_data = \'\'\n+#if str( $advanced_options.advanced_options_selector ) == "advanced":\n+ #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":\n+ #set pasted_data = \'\\t\'.join( str( $advanced_options.exclude_read_group[\'read_groups\'] ).split() )\n+ #end if\n+#end if\n+${pasted_data}\n+]]>\n+ </configfile>\n+ <configfile name="pasted_regions">\n+<![CDATA[\n+#set pasted_data = \'\'\n+#if str( $advanced_options.advanced_options_selector ) == "advanced":\n+ #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":\n+ #set pasted_data = \'\\t\'.join( str( $advanced_options.limit_by_region[\'region_paste\'] ).split() )\n+ #end if\n+#end if\n+${pasted_data}\n+]]>\n+ </configfile>\n+ </configfiles>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 samtools_wrapper.py --- a/samtools_wrapper.py Thu Mar 27 15:27:36 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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( '<html>\n<head>\n<title>Galaxy - SAMTOOLS Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' ) - for fname in sorted( os.listdir( dir ) ): - html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) - html_out.write( '</ul>\n</body>\n</html>\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__() |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam |
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| Binary file test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam has changed |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/phiX.bam |
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| Binary file test-data/phiX.bam has changed |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/phiX_1.bam |
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| Binary file test-data/phiX_1.bam has changed |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/samtools_mpileup_in_1.bam |
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| Binary file test-data/samtools_mpileup_in_1.bam has changed |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 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 Tue Apr 21 16:29:10 2015 -0400 |
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| @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000 |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 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 Tue Apr 21 16:29:10 2015 -0400 |
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| @@ -0,0 +1,43 @@ +phiX174 1411 A 0 1 +phiX174 1412 G 0 2,1,1 +phiX174 1413 C 0 3,2,2,1,1 +phiX174 1414 G 0 4,3,3,2,2,1 +phiX174 1415 C 0 5,4,4,3,3,2,1 +phiX174 1416 C 0 6,5,5,4,4,3,2,1 +phiX174 1417 G 0 7,6,6,5,5,4,3,2,1 +phiX174 1418 T 0 8,7,7,6,6,5,4,3,2,1 +phiX174 1419 G 0 9,8,8,7,7,6,5,4,3,2 +phiX174 1420 G 0 10,9,9,8,8,7,6,5,4,3 +phiX174 1421 A 0 11,10,10,9,9,8,7,6,5,4 +phiX174 1422 T 0 12,11,11,10,10,9,8,7,6,5 +phiX174 1423 G 0 13,12,12,11,11,10,9,8,7,6 +phiX174 1424 C 0 14,13,13,12,12,11,10,9,8,7 +phiX174 1425 C 0 15,14,14,13,13,12,11,10,9,8 +phiX174 1426 T 0 16,15,15,14,14,13,12,11,10,9 +phiX174 1427 G 0 17,16,16,15,15,14,13,12,11,10 +phiX174 1428 A 0 18,17,17,16,16,15,14,13,12,11 +phiX174 1429 C 0 19,18,18,17,17,16,15,14,13,12 +phiX174 1430 C 0 20,19,19,18,18,17,16,15,14,13 +phiX174 1431 G 0 21,20,20,19,19,18,17,16,15,14 +phiX174 1432 T 0 22,21,21,20,20,19,18,17,16,15 +phiX174 1433 A 0 23,22,22,21,21,20,19,18,17,16 +phiX174 1434 C 0 24,23,23,22,22,21,20,19,18,17 +phiX174 1435 C 0 25,24,24,23,23,22,21,20,19,18 +phiX174 1436 G 0 26,25,25,24,24,23,22,21,20,19 +phiX174 1437 A 0 27,26,26,25,25,24,23,22,21,20 +phiX174 1438 G 0 28,27,27,26,26,25,24,23,22,21 +phiX174 1439 G 0 29,28,28,27,27,26,25,24,23,22 +phiX174 1440 C 0 30,29,29,28,28,27,26,25,24,23 +phiX174 1441 T 0 31,30,30,29,29,28,27,26,25,24 +phiX174 1442 A 0 32,31,31,30,30,29,28,27,26,25 +phiX174 1443 A 0 33,32,32,31,31,30,29,28,27,26 +phiX174 1444 C 0 34,33,33,32,32,31,30,29,28,27 +phiX174 1445 C 0 34,33,34,32,33,32,31,30,29,28 +phiX174 1446 C 0 35,34,35,33,34,33,32,31,30,29 +phiX174 1447 T 0 36,35,36,34,35,34,33,32,31,30 +phiX174 1448 A 0 36,35,36,35,34,33,32,31 +phiX174 1449 A 0 36,36,35,34,33,32 +phiX174 1450 T 0 36,35,34,33 +phiX174 1451 G 0 36,35,34 +phiX174 1452 A 0 36,35 +phiX174 1453 G 0 36 |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 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 Tue Apr 21 16:29:10 2015 -0400 |
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| @@ -0,0 +1,3 @@ +[fai_load] build FASTA index. +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000 |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/samtools_mpileup_out_2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_2.vcf Tue Apr 21 16:29:10 2015 -0400 |
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| @@ -0,0 +1,22 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##samtoolsVersion=1.1+htslib-1.1 +##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat +##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat +##contig=<ID=phiX174,length=5386> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> +##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat |
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| diff -r 973fea5b4bdf -r c6fdfe3331d6 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 Tue Apr 21 16:29:10 2015 -0400 |
| [ |
| @@ -0,0 +1,2 @@ +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000 |
| b |
| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/samtools_mpileup_out_4.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_4.log Tue Apr 21 16:29:10 2015 -0400 |
| [ |
| @@ -0,0 +1,2 @@ +[mpileup] 1 samples in 1 input files +<mpileup> Set max per-file depth to 8000 |
| b |
| diff -r 973fea5b4bdf -r c6fdfe3331d6 test-data/samtools_mpileup_out_4.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_4.vcf Tue Apr 21 16:29:10 2015 -0400 |
| b |
| @@ -0,0 +1,22 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##samtoolsVersion=1.1+htslib-1.1 +##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa -C 0 -d 200 -E -q 0 -Q 43 -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_756.dat /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat +##reference=file:///var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa +##contig=<ID=phiX174,length=5386> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> +##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat |
| b |
| diff -r 973fea5b4bdf -r c6fdfe3331d6 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 27 15:27:36 2014 -0400 +++ b/tool_dependencies.xml Tue Apr 21 16:29:10 2015 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |