# HG changeset patch # User rnateam # Date 1450366267 18000 # Node ID 84d743632f5aef38149d3ab5357192ea1d48b1e4 # Parent 58d93900b3d194e054dc6f92db8e65105aabd4f9 Uploaded diff -r 58d93900b3d1 -r 84d743632f5a flexbar_dsc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar_dsc.xml Thu Dec 17 10:31:07 2015 -0500 @@ -0,0 +1,477 @@ + + + + + + + + + flexible barcode and adapter removal + + + flexbar + + + flexbar --version + + + + flexbar + + --threads \${GALAXY_SLOTS:-1} + + --reads $reads + + #if $cReads2.select == "on": + #if $cReads2.reads2.ext == $reads.ext: + --reads2 $cReads2.reads2 + #end if + #end if + + #if $reads.ext == "fastqsanger": + --format sanger + #end if + #if $reads.ext == "fastqsolexa": + --format solexa + #end if + #if $reads.ext == "fastqillumina": + --format i1.3 + #end if + #if $reads.ext == "csfasta": + --color-space + #end if + #if $reads.ext == "fastqcssanger": + --color-space + #end if + + + --max-uncalled $maxUncalled + --min-read-length $minReadLen + + #if $trimEnds.select == "on": + --pre-trim-left $trimEnds.trimLeft + --pre-trim-right $trimEnds.trimRight + #end if + + #if $cTrimPhred.select == "on": + --pre-trim-phred $cTrimPhred.trimPhred + #end if + + #if $cTrimLen.select == "on": + --post-trim-length $cTrimLen.trimLen + #end if + + + #if $cBarcodes.select == "on": + --barcodes $cBarcodes.barcodes + + #if $cBarcodes.cbReads.select == "yes": + --barcode-reads $cBarcodes.cbReads.bReads + #end if + + #if $cBarcodes.cbReads.select == "no": + $cBarcodes.cbReads.bKeep + #end if + + $cBarcodes.bUnassigned + + --barcode-trim-end $cBarcodes.bTrimEnd + + #if $cBarcodes.cbTailLen.select == "yes": + --barcode-tail-length $cBarcodes.cbTailLen.bTailLen + #end if + + #if $cBarcodes.cbMinOverlap.select == "yes": + --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap + #end if + + --barcode-threshold $cBarcodes.bThresh + + #if $cBarcodes.cbAlignScores.select == "yes": + --barcode-match $bMatch + --barcode-mismatch $bMismatch + --barcode-gap $bGap + #end if + #end if + + + #if $cAdapters.select == "on": + + #if $cAdapters.ccAdapters.select == "data": + --adapters $cAdapters.ccAdapters.adaptersData + #end if + + #if $cAdapters.ccAdapters.select == "seq": + --adapter-seq $cAdapters.ccAdapters.adapterSeq + #end if + + --adapter-trim-end $cAdapters.aTrimEnd + + #if $cAdapters.caTailLen.select == "yes": + --adapter-tail-length $cAdapters.caTailLen.aTailLen + #end if + + $cAdapters.aReadSet + + --adapter-min-overlap $cAdapters.aMinOverlap + --adapter-threshold $cAdapters.aThresh + + #if $cAdapters.caAlignScores.select == "yes": + --adapter-match $aMatch + --adapter-mismatch $aMismatch + --adapter-gap $aGap + #end if + #end if + + + #if $cOutput.select == "show": + $cOutput.fastaOutput + $cOutput.lenDist + $cOutput.singleReads + #end if + + #if $cLogging.select == "show": + $cLogging.logLevel + $cLogging.numTags + $cLogging.remTags + $cLogging.rndTags + #end if + + --target FlexbarOutput + && + for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done && + for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** + +Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. Flexbar is available on the project_ page. + +.. _project: https://github.com/seqan/flexbar + +------ + +**Trim-end modes** + +**Any:** longer side of read remains after overlap removal + +**Left:** right side remains after removal, align before or at read end + +**Right:** left part remains after removal, align after or at read start + +**Left tail:** consider first n bases of reads in alignment + +**Right tail:** use only last n bases, see tail-length options + +------ + +**Documentation** + +Further documentation is available on the `manual`__ wiki page and via the command line help screen. + +.. __: https://github.com/seqan/flexbar/wiki + +------ + +**Reference** + +Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. + + + +