| Previous changeset 32:e14f681ac3cc (2016-08-10) Next changeset 34:7d7473434ce9 (2016-08-10) |
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Commit message:
Deleted selected files |
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removed:
enhanced_bowtie_wrapper.xml |
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| diff -r e14f681ac3cc -r 5ef807f03047 enhanced_bowtie_wrapper.xml --- a/enhanced_bowtie_wrapper.xml Wed Aug 10 12:24:19 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,987 +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-\t\t#if $singlePaired.pParams.pSettingsType == "full":\n-\t\t\t--filetype="${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 $singlePaired.pParams.pSettingsType == "full":\n-\t\t\t--outtype="${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' |