# HG changeset patch # User jtilman # Date 1356911055 18000 # Node ID 589b4866f537c3e596c67e1e9e8cc7b9d9d23a6d # Parent c0c9b43670d075628fdc3150d7ef6dd99de77aea Uploaded Flexbar galaxy tool definition file flexbar.xml diff -r c0c9b43670d0 -r 589b4866f537 flexbar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.xml Sun Dec 30 18:44:15 2012 -0500 @@ -0,0 +1,398 @@ + + + + + + flexible barcode and adapter removal + + + 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://sourceforge.net/p/flexbar/wiki + + + +