| Previous changeset 0:0c7e4eadfb3c (2012-11-26) Next changeset 2:42c4463baaad (2014-01-16) |
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Commit message:
Updated command line format per dev team standards. |
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modified:
bowtie_wrapper.xml |
| b |
| diff -r 0c7e4eadfb3c -r e1c59c194b7b bowtie_wrapper.xml --- a/bowtie_wrapper.xml Mon Nov 26 09:43:28 2012 -0500 +++ b/bowtie_wrapper.xml Mon Apr 01 14:36:33 2013 -0400 |
| b |
| b'@@ -9,30 +9,30 @@\n ## Hackish setting of number of threads\n --threads="4"\n ## Outputs\n- --output=$output\n+ --output="${output}"\n #if str( $singlePaired.sPaired ) == "single"\n #if $output_unmapped_reads_l\n- --output_unmapped_reads=$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+ --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=$output_unmapped_reads_r\n+ --output_unmapped_reads_l="${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=$output_suppressed_reads_r\n+ --output_suppressed_reads_l="${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+ --suppressHeader="${suppressHeader}"\n+ --genomeSource="${refGenomeSource.genomeSource}"\n #if $refGenomeSource.genomeSource == "history":\n ##index already exists\n #if $refGenomeSource.ownFile.extension.startswith( \'bowtie_\' ):\n@@ -41,91 +41,91 @@\n --do_not_build_index\n #else:\n ##build index on the fly\n- --ref=$refGenomeSource.ownFile\n- --indexSettings=$refGenomeSource.indexParams.indexSettings\n+ --ref="${refGenomeSource.ownFile}"\n+ --indexSettings="${refGenomeSource.indexParams.indexSettings}"\n #if $refGenomeSource.indexParams.indexSettings == "indexFull":\n- --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB\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=$refGenomeSource.indexParams.autoBehavior.dcv\n+ --ipacked="${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- --icutoff=$refGenomeSource.indexParams.cutoff \n+ --inodc="${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.i'..b'axBacktracks}"\n+ --strata="${singlePaired.sParams.sBestOption.sdStrata}"\n #else:\n- --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks\n+ --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}"\n #end if\n- --offrate=$singlePaired.sParams.sOffrate\n- --seed=$singlePaired.sParams.sSeed\n+ --offrate="${singlePaired.sParams.sOffrate}"\n+ --seed="${singlePaired.sParams.sSeed}"\n #end if\n #else:\n- --input1=$singlePaired.pInput1\n- --input2=$singlePaired.pInput2\n- --maxInsert=$singlePaired.pMaxInsert\n- --mateOrient=$singlePaired.pMateOrient\n- --params=$singlePaired.pParams.pSettingsType\n+ --input1="${singlePaired.pInput1}"\n+ --input2="${singlePaired.pInput2}"\n+ --maxInsert="${singlePaired.pMaxInsert}"\n+ --mateOrient="${singlePaired.pMateOrient}"\n+ --params="${singlePaired.pParams.pSettingsType}"\n #if $singlePaired.pParams.pSettingsType == "full":\n- --skip=$singlePaired.pParams.pSkip\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=$singlePaired.pParams.pRounding\n- --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign\n- --minInsert=$singlePaired.pParams.pMinInsert\n- --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt\n- --forwardAlign=$singlePaired.pParams.pForwardAlign\n- --reverseAlign=$singlePaired.pParams.pReverseAlign\n- --tryHard=$singlePaired.pParams.pTryHard\n- --valAlign=$singlePaired.pParams.pValAlign\n- --allValAligns=$singlePaired.pParams.pAllValAligns\n- --suppressAlign=$singlePaired.pParams.pSuppressAlign\n- --best=$singlePaired.pParams.pBestOption.pBest\n+ --skip="${singlePaired.pParams.pSkip}"\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="${singlePaired.pParams.pRounding}"\n+ --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}"\n+ --minInsert="${singlePaired.pParams.pMinInsert}"\n+ --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}"\n+ --forwardAlign="${singlePaired.pParams.pForwardAlign}"\n+ --reverseAlign="${singlePaired.pParams.pReverseAlign}"\n+ --tryHard="${singlePaired.pParams.pTryHard}"\n+ --valAlign="${singlePaired.pParams.pValAlign}"\n+ --allValAligns="${singlePaired.pParams.pAllValAligns}"\n+ --suppressAlign="${singlePaired.pParams.pSuppressAlign}"\n+ --best="${singlePaired.pParams.pBestOption.pBest}"\n #if $singlePaired.pParams.pBestOption.pBest == "doBest":\n- --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks\n- --strata=$singlePaired.pParams.pBestOption.pdStrata\n+ --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}"\n+ --strata="${singlePaired.pParams.pBestOption.pdStrata}"\n #else:\n- --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks\n+ --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}"\n #end if\n- --offrate=$singlePaired.pParams.pOffrate\n- --seed=$singlePaired.pParams.pSeed\n+ --offrate="${singlePaired.pParams.pOffrate}"\n+ --seed="${singlePaired.pParams.pSeed}"\n #end if\n #end if\n </command>\n' |