| Previous changeset 3:9ca609a2a421 (2014-02-21) Next changeset 5:306077e393d4 (2016-08-18) |
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Commit message:
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty |
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modified:
bowtie_wrapper.py bowtie_wrapper.xml tool_dependencies.xml |
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| diff -r 9ca609a2a421 -r df86f29bedee bowtie_wrapper.py --- a/bowtie_wrapper.py Fri Feb 21 12:40:39 2014 -0500 +++ b/bowtie_wrapper.py Tue Jul 21 13:04:45 2015 -0400 |
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| b'@@ -27,10 +27,10 @@\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, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy\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, --valAlign=v: Report up to n valid arguments per read\n- -V, --allValAligns=V: Whether or not to report all valid alignments per read\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@@ -59,7 +59,6 @@\n -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As\n -N, --iendian=N: Endianness to use when serializing integers to the index file\n -Z, --iseed=Z: Seed for the pseudorandom number generator\n- -c, --icutoff=c: Number of first bases of the reference sequence to index\n -x, --indexSettings=x: Whether or not indexing options are to be set\n -H, --suppressHeader=H: Suppress header\n --do_not_build_index: Flag to specify that provided file is already indexed and to just use \'as is\'\n@@ -101,10 +100,10 @@\n parser.add_option( \'-M\', \'--mismatchQual\', dest=\'mismatchQual\', help=\'Maximum permitted total of quality values at mismatched read positions\' )\n parser.add_option( \'-l\', \'--seedLen\', dest=\'seedLen\', help=\'Seed length\' )\n parser.add_option( \'-n\', \'--rounding\', dest=\'rounding\', help=\'Whether or not to round to the nearest 10 and saturating at 30\' )\n- parser.add_option( \'-P\', \'--maqSoapAlign\', dest=\'maqSoapAlign\', help=\'Choose MAQ- or SOAP-like alignment policy\' )\n+ parser.add_option( \'-P\', \'--maxMismatches\', dest=\'maxMismatches\', help=\'Maximum number of mismatches for -v alignment mode\' )\n parser.add_option( \'-w\', \'--tryHard\', dest=\'tryHard\', help=\'Whether or not to try as hard as possible to find valid alignments when they exist\' )\n- parser.add_option( \'-v\', \'--valAlign\', dest=\'valAlign\', help=\'Report up to n valid arguments per read\' )\n- parser.add_option( \'-V\', \'--allValAligns\', dest=\'allValAligns\', help=\'Whether or not to report all valid alignments per read\' )\n+ parser.add_option( \'-V\', \'--allValAligns\', dest=\'allValAligns\', help=\'Whether or not to report all valid alignments per read or pair\' )\n+ parser.add_option( \'-v\', \'--valAlign\', dest=\'valAlign\', help=\'Report up to n valid alignments per read or pair\' )\n parser.add_option( \'-G\', \'--suppressAlign\', dest=\'suppressAlign\', help=\'Suppress all alignments for a read if more than n reportable alignments exist\' )\n parser.add_option( \'-b\', \'--best\', dest=\'best\', help="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 parser.add_option( \'-B\', \'--maxBacktracks\', dest=\'maxBacktracks\', help=\'Maximum number of backtracks permitted when aligning a read\' )\n@@ -133,12 +132,13 @@\n parser.add_option( \'-X\', \'--intoa\', dest=\'intoa\', help=\'Whether or not to convert Ns in the reference sequence to As\' )\n parser.add_option( \'-N\', \'--iendian\', dest=\'iendian\', help=\'Endianness to use when serializing integers to the index file\' )\n parser.add_option( \'-Z\', \'--iseed\', dest=\'iseed\', help=\'Seed for the pseudorandom number generator\' )\n- parser.add_option( \'-c\', \'--icutoff\', dest=\'icutoff\', help=\'Numb'..b' else:\n ibmaxdivn = \'\'\n- if options.idcv and int( options.idcv ) > 0:\n+ if options.idcv and int( options.idcv ) >= 3:\n idcv = \'--dcv %s\' % options.idcv\n else:\n idcv = \'\'\n@@ -183,7 +183,7 @@\n inoref = \'--noref\'\n else:\n inoref = \'\'\n- if options.iftab and int( options.iftab ) >= 0:\n+ if options.iftab and int( options.iftab ) >= 1:\n iftab = \'--ftabchars %s\' % options.iftab\n else:\n iftab = \'\'\n@@ -199,14 +199,10 @@\n iseed = \'--seed %s\' % options.iseed\n else:\n iseed = \'\'\n- if options.icutoff and int( options.icutoff ) > 0:\n- icutoff = \'--cutoff %s\' % options.icutoff\n- else:\n- icutoff = \'\'\n- indexing_cmds = \'%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s\' % \\\n- ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc, \n- inoref, options.ioffrate, iftab, intoa, iendian, \n- iseed, icutoff, colorspace )\n+ indexing_cmds = \'%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s\' % \\\n+ ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,\n+ inoref, options.ioffrate, iftab, intoa, iendian,\n+ iseed, colorspace )\n except ValueError, e:\n # clean up temp dir\n if os.path.exists( tmp_index_dir ):\n@@ -283,16 +279,17 @@\n trimL = \'-3 %s\' % options.trimL\n else:\n trimL = \'\'\n- if options.maqSoapAlign != \'-1\' and int( options.maqSoapAlign ) >= 0:\n- maqSoapAlign = \'-v %s\' % options.maqSoapAlign\n+ if options.maxMismatches and (options.maxMismatches == \'0\' or options.maxMismatches == \'1\' \\\n+ or options.maxMismatches == \'2\' or options.maxMismatches == \'3\'):\n+ maxMismatches = \'-v %s\' % options.maxMismatches\n else:\n- maqSoapAlign = \'\'\n+ maxMismatches = \'\'\n if options.mismatchSeed and (options.mismatchSeed == \'0\' or options.mismatchSeed == \'1\' \\\n or options.mismatchSeed == \'2\' or options.mismatchSeed == \'3\'):\n mismatchSeed = \'-n %s\' % options.mismatchSeed\n else:\n mismatchSeed = \'\'\n- if options.mismatchQual and int( options.mismatchQual ) >= 0:\n+ if options.mismatchQual and int( options.mismatchQual ) >= 1:\n mismatchQual = \'-e %s\' % options.mismatchQual\n else:\n mismatchQual = \'\'\n@@ -395,8 +392,8 @@\n aligning_cmds = \'-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s \' \\\n \'%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s \' % \\\n ( maxInsert, mateOrient, options.threads, suppressHeader,\n- colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign,\n- mismatchSeed, mismatchQual, seedLen, rounding, minInsert, \n+ colorspace, skip, alignLimit, trimH, trimL, maxMismatches,\n+ mismatchSeed, mismatchQual, seedLen, rounding, minInsert,\n maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,\n tryHard, valAlign, allValAligns, suppressAlign, best,\n strata, offrate, seed, snpphred, snpfrac, keepends,\n@@ -466,4 +463,5 @@\n stdout += \'Sequence file aligned.\\n\'\n sys.stdout.write( stdout )\n \n-if __name__=="__main__": __main__()\n+if __name__ == "__main__":\n+ __main__()\n' |
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| diff -r 9ca609a2a421 -r df86f29bedee bowtie_wrapper.xml --- a/bowtie_wrapper.xml Fri Feb 21 12:40:39 2014 -0500 +++ b/bowtie_wrapper.xml Tue Jul 21 13:04:45 2015 -0400 |
| [ |
| b'@@ -1,9 +1,9 @@\n-<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2">\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+ <requirement type="package" version="0.12.7">bowtie</requirement>\n </requirements>\n <description></description>\n- <parallelism method="basic"></parallelism>\n+ <version_command>bowtie --version</version_command>\n <command interpreter="python">\n bowtie_wrapper.py\n ## Set number of threads\n@@ -58,7 +58,6 @@\n --intoa="${refGenomeSource.indexParams.ntoa}"\n --iendian="${refGenomeSource.indexParams.endian}"\n --iseed="${refGenomeSource.indexParams.seed}"\n- --icutoff="${refGenomeSource.indexParams.cutoff}"\n #end if\n #end if\n #else\n@@ -74,21 +73,32 @@\n --alignLimit="${singlePaired.sParams.sAlignLimit}"\n --trimH="${singlePaired.sParams.sTrimH}"\n --trimL="${singlePaired.sParams.sTrimL}"\n- --mismatchSeed="${singlePaired.sParams.sMismatchSeed}"\n- --mismatchQual="${singlePaired.sParams.sMismatchQual}"\n- --seedLen="${singlePaired.sParams.sSeedLen}"\n- --rounding="${singlePaired.sParams.sRounding}"\n- --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}"\n- --tryHard="${singlePaired.sParams.sTryHard}"\n- --valAlign="${singlePaired.sParams.sValAlign}"\n- --allValAligns="${singlePaired.sParams.sAllValAligns}"\n+ #if $singlePaired.sParams.alignModeOption.alignMode == \'nMode\'\n+ --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"\n+ --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"\n+ --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"\n+ --rounding="${singlePaired.sParams.alignModeOption.sRounding}"\n+ #else\n+ --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"\n+ #end if\n+ --forwardAlign="${singlePaired.sParams.sForwardAlign}"\n+ --reverseAlign="${singlePaired.sParams.sReverseAlign}"\n+ --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"\n+ --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"\n+ #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"\n+ --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"\n+ #end if\n --suppressAlign="${singlePaired.sParams.sSuppressAlign}"\n --best="${singlePaired.sParams.sBestOption.sBest}"\n #if $singlePaired.sParams.sBestOption.sBest == "doBest":\n- --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}"\n --strata="${singlePaired.sParams.sBestOption.sdStrata}"\n+ #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"\n+ --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"\n+ #end if\n #else:\n- --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}"\n+ #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"\n+ --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"\n+ #end if\n #end if\n --offrate="${singlePaired.sParams.sOffrate}"\n --seed="${singlePaired.sParams.sSeed}"\n@@ -104,25 +114,35 @@\n --alignLimit="${singlePaired.pParams.pAlignLimit}"\n --trimH="${singlePaired.pParams.pTrimH}"\n --trimL="${singlePaired.pParams.pTrimL}"\n- --mismatchSeed="${singlePaired.pParams.pMismatchSeed}"\n- --mismatchQual="${singlePaired.pParams.pMismatchQual}"\n- --seedLen="${singlePaired.pParams.pSeedLen}"\n- --rounding="${singlePaired.pParams.pRounding}'..b' chrM_base is the index files\' location/base name. \n+ chrM_base is the index files\' location/base name.\n -->\n <param name="genomeSource" value="history" />\n <param name="ownFile" value="phiX.fasta" />\n@@ -648,7 +735,6 @@\n <param name="ntoa" value="no" />\n <param name="endian" value="little" />\n <param name="seed" value="-1" />\n- <param name="cutoff" value="-1" />\n <param name="sPaired" value="paired" />\n <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />\n <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />\n@@ -697,7 +783,7 @@\n The output is in SAM format, and has the following columns::\n \n Column Description\n- -------- -------------------------------------------------------- \n+ -------- --------------------------------------------------------\n 1 QNAME Query (pair) NAME\n 2 FLAG bitwise FLAG\n 3 RNAME Reference sequence NAME\n@@ -710,7 +796,7 @@\n 10 SEQ query SEQuence on the same strand as the reference\n 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)\n 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE\n- \n+\n The flags are as follows::\n \n Flag Description\n@@ -760,8 +846,8 @@\n -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The \n indexer will mark every 2^INT rows. The marked rows correspond to rows on \n the genome. [5]\n- -t INT Ftab. The lookup table used to calculate an initial Burrows-Wheeler range \n- with respect to the first INT characters of the query. Ftab is 4^INT+1 \n+ -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range \n+ with respect to the first INT characters of the query. Ftab size is 4^(INT+1) \n bytes. [10]\n --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are \n simply excluded from the index and Bowtie will not find alignments that \n@@ -769,8 +855,6 @@\n --big Endianness. Endianness to use when serializing integers to the index file. [off]\n --little Endianness. [--little]\n --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]\n- --cutoff INT Cutoff. Index only the first INT bases of the reference sequences (cumulative \n- across sequences) and ignore the rest. [off]\n \n For aligning (bowtie)::\n \n@@ -787,10 +871,10 @@\n at 30. [70]\n -l INT Seed length. The number of bases on the high-quality end of the read to \n which the -n ceiling applies. Must be at least 5. [28]\n- --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and \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+ -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@@ -835,5 +919,8 @@\n --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace \n alignments. [off]\n \n- </help>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1186/gb-2009-10-3-r25</citation>\n+ </citations>\n </tool>\n' |
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| diff -r 9ca609a2a421 -r df86f29bedee tool_dependencies.xml --- a/tool_dependencies.xml Fri Feb 21 12:40:39 2014 -0500 +++ b/tool_dependencies.xml Tue Jul 21 13:04:45 2015 -0400 |
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| @@ -1,6 +1,6 @@ <?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="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |