# HG changeset patch # User jtilman # Date 1356893875 18000 # Node ID 68a4edf205f37733aae5b93c60357a7369cfa054 Uploaded Flexbar tool definition file flexbar.xml diff -r 000000000000 -r 68a4edf205f3 flexbar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.xml Sun Dec 30 13:57:55 2012 -0500 @@ -0,0 +1,398 @@ + + + + + + flexible barcode and adapter processing + + + flexbar + + + flexbar --version + + + + flexbar.pl flexbar + + --threads 1 + + --reads $reads + + #if $cReads2.select == "on": + #if $cReads2.reads2.ext == $reads.ext: + --reads2 $cReads2.reads2 + #end if + #end if + + + #if $reads.ext == "fasta": + --format fasta + #end if + #if $reads.ext == "fastq": + --format fastq + #end if + #if $reads.ext == "fastqsanger": + --format fastq-sanger + #end if + #if $reads.ext == "fastqsolexa": + --format fastq-solexa + #end if + #if $reads.ext == "fastqillumina": + --format fastq-i1.3 + #end if + #if $reads.ext == "csfasta": + --format csfasta + #end if + #if $reads.ext == "fastqcssanger": + --format csfastq + #end if + + + --max-uncalled $maxUncalled + --min-readlength $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 + + --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 == "yes": + + #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 + + --adapter-min-overlap $cAdapters.aMinOverlap + --adapter-threshold $cAdapters.aThresh + + #if $cAdapters.caAlignScores.select == "on": + --adapter-match $aMatch + --adapter-mismatch $aMismatch + --adapter-gap $aGap + #end if + + #end if + + + #if $cLogging.select == "show" + $cLogging.logLevel + $cLogging.noLenDist + $cLogging.remTag + #end if + + #if $cLogging.select == "off" + --no-length-dist + #end if + + + $output $output.id $__new_file_path__ $reads.ext + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Flexbar help** + +Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases 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: https://sourceforge.net/projects/flexbar + +------ + +**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. + +------ + +**Trim-end modes** + +**Any:** longer part of read remains + +**Left:** align before or at read end, right part remains + +**Right:** align after or at read start, left part remains + +**Left tail:** consider first n bases, see tail-length options + +**Right tail:** use only last n bases of reads in alignment + +------ + +**Documentation** + +.. class:: warningmark + +Further documentation is available on the `manual`__ wiki and via the command line help screen. + +.. __: http://http://sourceforge.net/p/flexbar/wiki + + + +