| Previous changeset 3:4901e45ab80d (2016-08-07) Next changeset 5:386d8492cfc1 (2016-08-07) |
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Commit message:
Deleted selected files |
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removed:
enhanced_bowtie_wrapper 1.0.0.py enhanced_bowtie_wrapper 1.0.0.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 4901e45ab80d -r 43a534fe1cde enhanced_bowtie_wrapper 1.0.0.py --- a/enhanced_bowtie_wrapper 1.0.0.py Sun Aug 07 21:59:01 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,497 +0,0 @@\n-#!/usr/bin/env python\n-\n-"""\n-Runs Bowtie on single-end or paired-end data.\n-For use with Bowtie v. 0.12.7\n-\n-usage: bowtie_wrapper.py [options]\n- -t, --threads=t: The number of threads to run\n- -o, --output=o: The output file\n- --output_unmapped_reads=: File name for unmapped reads (single-end)\n- --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)\n- --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)\n- --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)\n- --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)\n- --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)\n- -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format\n- -I, --input2=I: The reverse reads file in Sanger FASTQ format\n- -4, --dataType=4: The type of data (SOLiD or Solexa)\n- -2, --paired=2: Whether the data is single- or paired-end\n- -g, --genomeSource=g: The type of reference provided\n- -r, --ref=r: The reference genome to use or index\n- -s, --skip=s: Skip the first n reads\n- -a, --alignLimit=a: Only align the first n reads\n- -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment\n- -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment\n- -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed\n- -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions\n- -l, --seedLen=l: Seed length\n- -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30\n- -P, --maxMismatches=P: Maximum number of mismatches for -v alignment mode\n- -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist\n- -V, --allValAligns=V: Whether or not to report all valid alignments per read or pair\n- -v, --valAlign=v: Report up to n valid alignments per read or pair\n- -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist\n- -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are \'best\' in terms of stratum and in terms of the quality values at the mismatched positions\n- -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read\n- -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable\n- -j, --minInsert=j: Minimum insert size for valid paired-end alignments\n- -J, --maxInsert=J: Maximum insert size for valid paired-end alignments\n- -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand\n- -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate\n- -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand\n- -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand\n- -F, --offrate=F: Override the offrate of the index to n\n- -8, --snpphred=8: SNP penalty on Phred scale\n- -6, --snpfrac=6: Fraction of sites expected to be SNP sites\n- -7, --keepends=7: Keep extreme-end nucleotides and qualities\n- -S, --seed=S: Seed for pseudo-random number generator\n- -C, --params=C: Whether to use default or specified parameters\n- -u, --iautoB=u: Automatic or specified behavior\n- -K, --ipacked=K: Whether or not to use a packed representation for DNA strings\n- -Q, --ibmax=Q: Maximum number of suffixes allowed in a block\n- -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference\n- -D, --idcv=D: The period for the differ'..b' tryHard, valAlign, allValAligns, suppressAlign, best,\n- strata, offrate, seed, snpphred, snpfrac, keepends,\n- output_unmapped_reads, output_suppressed_reads,\n- quality_score_encoding )\n- \n- \n- \n- \n- \n- \n- except ValueError, e:\n- # clean up temp dir\n- if os.path.exists( tmp_index_dir ):\n- shutil.rmtree( tmp_index_dir )\n- stop_err( \'Something is wrong with the alignment parameters and the alignment could not be run\\n\' + str( e ) )\n- try:\n- # have to nest try-except in try-finally to handle 2.4\n- try:\n- # prepare actual mapping commands\n- if options.paired == \'paired\':\n- cmd2 = \'bowtie %s %s -1 %s -2 %s > %s\' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )\n- else:\n- cmd2 = \'bowtie %s %s %s > %s\' % ( aligning_cmds, ref_file_name, options.input1, options.output )\n- # align\n- tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name\n- tmp_stderr = open( tmp, \'wb\' )\n- proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )\n- returncode = proc.wait()\n- tmp_stderr.close()\n- # get stderr, allowing for case where it\'s very large\n- tmp_stderr = open( tmp, \'rb\' )\n- stderr = \'\'\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read( buffsize )\n- if not stderr or len( stderr ) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- tmp_stderr.close()\n- if returncode != 0:\n- raise Exception, stderr\n- # get suppressed and unmapped reads output files in place if appropriate\n- if options.paired == \'paired\' and tmp_suppressed_file_name and \\\n- options.output_suppressed_reads_l and options.output_suppressed_reads_r:\n- try:\n- left = tmp_suppressed_file_name.replace( \'.fastq\', \'_1.fastq\' )\n- right = tmp_suppressed_file_name.replace( \'.fastq\', \'_1.fastq\' )\n- shutil.move( left, options.output_suppressed_reads_l )\n- shutil.move( right, options.output_suppressed_reads_r )\n- except Exception, e:\n- sys.stdout.write( \'Error producing the suppressed output file.\\n\' )\n- if options.paired == \'paired\' and tmp_unmapped_file_name and \\\n- options.output_unmapped_reads_l and options.output_unmapped_reads_r:\n- try:\n- left = tmp_unmapped_file_name.replace( \'.fastq\', \'_1.fastq\' )\n- right = tmp_unmapped_file_name.replace( \'.fastq\', \'_2.fastq\' )\n- shutil.move( left, options.output_unmapped_reads_l )\n- shutil.move( right, options.output_unmapped_reads_r )\n- except Exception, e:\n- sys.stdout.write( \'Error producing the unmapped output file.\\n\' )\n- # check that there are results in the output file\n- if os.path.getsize( options.output ) == 0:\n- raise Exception, \'The output file is empty, there may be an error with your input file or settings.\'\n- except Exception, e:\n- stop_err( \'Error aligning sequence. \' + str( e ) )\n- finally:\n- # clean up temp dir\n- if os.path.exists( tmp_index_dir ):\n- shutil.rmtree( tmp_index_dir )\n- stdout += \'Sequence file aligned.\\n\'\n- sys.stdout.write( stdout )\n-\n-if __name__ == "__main__":\n- __main__()\n' |
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| diff -r 4901e45ab80d -r 43a534fe1cde enhanced_bowtie_wrapper 1.0.0.xml --- a/enhanced_bowtie_wrapper 1.0.0.xml Sun Aug 07 21:59:01 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,977 +0,0 @@\n-<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3">\n- <requirements>\n- <requirement type="package" version="0.12.7">bowtie</requirement>\n- </requirements>\n- <description></description>\n- <version_command>bowtie --version</version_command>\n- <command interpreter="python">\n- bowtie_wrapper.py\n- ## Set number of threads\n- --threads="\\${GALAXY_SLOTS:-4}"\n- ## Outputs\n- \n- \n-\n-\n- #if "${singlePaired.sParams.outtype}" == "S"\n- --output="${outputS}"\n- #else\n- --output="${outputM}"\n- #end if\n-\n- \n- \n- #if str( $singlePaired.sPaired ) == "single"\n- #if $output_unmapped_reads_l\n- --output_unmapped_reads="${output_unmapped_reads_l}"\n- #end if\n- #if $output_suppressed_reads_l\n- --output_suppressed_reads="${output_suppressed_reads_l}"\n- #end if\n- --galaxy_input_format="${singlePaired.sInput1.ext}"\n- #else\n- #if $output_unmapped_reads_l and $output_unmapped_reads_r\n- --output_unmapped_reads_l="${output_unmapped_reads_l}"\n- --output_unmapped_reads_r="${output_unmapped_reads_r}"\n- #end if\n- #if $output_suppressed_reads_l and $output_suppressed_reads_l\n- --output_suppressed_reads_l="${output_suppressed_reads_l}"\n- --output_suppressed_reads_r="${output_suppressed_reads_r}"\n- #end if\n- --galaxy_input_format="${singlePaired.pInput1.ext}"\n- #end if\n- ## Inputs\n- --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper\n- --suppressHeader="${suppressHeader}"\n- --genomeSource="${refGenomeSource.genomeSource}"\n- #if $refGenomeSource.genomeSource == "history":\n- ##index already exists\n- #if $refGenomeSource.ownFile.extension.startswith( \'bowtie_\' ):\n- ##user previously built\n- --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"\n- --do_not_build_index\n- #else:\n- ##build index on the fly\n- --ref="${refGenomeSource.ownFile}"\n- --indexSettings="${refGenomeSource.indexParams.indexSettings}"\n- #if $refGenomeSource.indexParams.indexSettings == "indexFull":\n- --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"\n- #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":\n- --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"\n- --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"\n- --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"\n- --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"\n- #end if\n- --inodc="${refGenomeSource.indexParams.nodc}"\n- --inoref="${refGenomeSource.indexParams.noref}"\n- --ioffrate="${refGenomeSource.indexParams.offrate}"\n- --iftab="${refGenomeSource.indexParams.ftab}"\n- --intoa="${refGenomeSource.indexParams.ntoa}"\n- --iendian="${refGenomeSource.indexParams.endian}"\n- --iseed="${refGenomeSource.indexParams.seed}"\n- #end if\n- #end if\n- #else\n- ##use pre-built index\n- --ref="${refGenomeSource.index.fields.path}"\n- #end if\n- --paired="${singlePaired.sPaired}"\n- #if $singlePaired.sPaired == "single":\n- \n- \n- \n- \n- \n- --filetype="${singlePaired.sParams.filetype}" \n- --outtype="${singlePaired.sParams.outtype}"\n- \n- \n- \n- --input1="${singlePaired.sInput1}"\n- --params="${singlePaired.sParams.sSettingsType}"\n- #if $singlePaired.sParams.sSettingsType == "full":\n- --skip="${singlePaired.sParams.sSkip}"\n- --alignLimit="${singlePaired.sParams.sAlignLimit}"\n- --trimH="${singlePaired.sParams.sTrimH}"\n- --trimL="${singlePaired.sParams.sTrimL}"\n'..b' ceiling applies. Must be at least 5. [28]\n- --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and \n- saturate at 30. This options turns off that rounding. [off] \n- -v INT Maq- or SOAP-like alignment policy. This option turns off the default \n- Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments \n- with at most INT mismatches. [off]\n- -I INT Minimum insert. The minimum insert size for valid paired-end alignments. \n- Does checking on untrimmed reads if -5 or -3 is used. [0]\n- -X INT Maximum insert. The maximum insert size for valid paired-end alignments. \n- Does checking on untrimmed reads if -5 or -3 is used. [250]\n- --fr Mate orientation. The upstream/downstream mate orientations for a valid \n- paired-end alignment against the forward reference strand. [--fr]\n- --rf Mate orientation. [off]\n- --ff Mate orientation. [off]\n- --pairtries INT Maximum alignment attempts for paired-end data. [100] \n- --nofw No forward aligning. Choosing this option means that Bowtie will not attempt \n- to align against the forward reference strand. [off]\n- --norc No reverse-complement aligning. Setting this will mean that Bowtie will not \n- attempt to align against the reverse-complement reference strand. [off]\n- --un FILENAME Write all reads that could not be aligned to file [off]\n- --max FILENAME Write all reads with a number of valid alignments exceeding the limit\n- set with the -m option to file [off]\n- --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning \n- a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]\n- -y Try hard. Try as hard as possible to find valid alignments when they exist, \n- including paired-end alignments. [off]\n- --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to \n- store path descriptors in --best mode. [32]\n- -k INT Valid alignments. The number of valid alignments per read or pair. [off] \n- -a All valid alignments. Choosing this means that all valid alignments per read \n- or pair will be reported. [off]\n- -m INT Suppress alignments. Suppress all alignments for a particular read or pair \n- if more than INT reportable alignments exist for it. [no limit]\n- --best Best mode. Make Bowtie guarantee that reported singleton alignments are \n- "best" in terms of stratum (the number of mismatches) and quality values at \n- mismatched position. [off]\n- --strata Best strata. When running in best mode, report alignments that fall into the \n- best stratum if there are ones falling into more than one. [off]\n- -o INT Offrate override. Override the offrate of the index with INT. Some row \n- markings are discarded when index read into memory. INT must be greater than \n- the value used to build the index (default: 5). [off]\n- --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]\n- --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of \n- SNPs per base in the subject genome. [see --snpfrac]\n- --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace \n- alignments. [0.001]\n- --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace \n- alignments. [off]\n-\n- </help>\n-</tool>\n' |
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| diff -r 4901e45ab80d -r 43a534fe1cde tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sun Aug 07 21:59:01 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Locations of indexes in the Bowtie mapper format --> - <table name="bowtie_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bowtie_indices.loc" /> - </table> -</tables> |
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| diff -r 4901e45ab80d -r 43a534fe1cde tool_dependencies.xml --- a/tool_dependencies.xml Sun Aug 07 21:59:01 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |