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enhanced_bowtie_wrapper.xml |
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| diff -r 5ef807f03047 -r 7d7473434ce9 enhanced_bowtie_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/enhanced_bowtie_wrapper.xml Wed Aug 10 12:29:45 2016 -0400 |
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| b'@@ -0,0 +1,987 @@\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+\t\t#if $singlePaired.sParams.sSettingsType == "full":\n+\t\t\t--filetype="${singlePaired.sParams.filetype}"\n+\t\t#else\n+\t\t\t--filetype="q"\n+\t\t#end if\n+\t\t\n+\t\t#if $singlePaired.sParams.sSettingsType == "full":\n+\t\t\t--outtype="${singlePaired.sParams.outtype}"\n+\t\t#else\n+\t\t\t--outtype="S"\n+\t\t#end if\n+\n+\n+\n+ \n+ \n+ --input1="${singlePaired.sInput1}"\n+ --params="${singlePaired.sParams.sSettingsType}"\n+ #if $singlePaired.sParams.sSettingsType == "full":\n+ --skip="${singlePaired.sParams.sSkip}"\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' |