# HG changeset patch # User rnateam # Date 1448616782 18000 # Node ID 258b6f9e19ab6c466138e5c9976de17a513edec2 # Parent 55b539a509f09a3b22b8b51ee16c2669b8f3ee7d Uploaded diff -r 55b539a509f0 -r 258b6f9e19ab flexbar.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.pl Fri Nov 27 04:33:02 2015 -0500 @@ -0,0 +1,49 @@ +#!/usr/bin/env perl + +# Flexbar wrapper for Galaxy tool definition, version 2.5 +# Author: Johannes Roehr + +use warnings; +use strict; + +# this parses the last 4 arguments +# what is id -> xml $output.id +# what is folder -> xml $__new_file_path__ +# what is format? -> xml $reads.ext +my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV]; + +# this parses all but the last four arguments +# contains the call to the flexbar actual +my $call = join " ", @ARGV[0..($#ARGV - 4)]; + +# this calls flexbar and +# prefix for output files will be "FlexbarTargetFile" +system $call .' --target FlexbarTargetFile > '. $outFile and exit 1; + +# now we parse all output files +foreach(){ + + # determine filetype + my $fileType; + + $fileType = $1 if /\.(\w+)$/; + $fileType = $format if /\.\w*fast\w$/; + $fileType = 'fasta' if /\.fasta$/; + $fileType = 'csfasta' if /\.csfasta$/; + $fileType = 'tabular' if /\.lengthdist$/; + + # this is just the filename from the for loop + my $file = $_; + + # replace underscores by minus in $_ + s/_/-/g; + + # set new name for output files + my $name = "primary_". $id ."_". $_ ."_visible_". $fileType; + + # rename output file to a pattern recognized by flexbar? + rename $file, $name; + # best guess: this seems to move the file into a folder + # rename behavious is not specified by perl... or implementation differs. + rename $name, $folder; +} diff -r 55b539a509f0 -r 258b6f9e19ab flexbar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.xml Fri Nov 27 04:33:02 2015 -0500 @@ -0,0 +1,466 @@ + + + + + + + + + flexible barcode and adapter removal + + + flexbar + + + flexbar --version + + + + flexbar.pl 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 + + + $output $output.id $__new_file_path__ $reads.ext + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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. + + + + diff -r 55b539a509f0 -r 258b6f9e19ab flexbar_split_RYYR_bcs.xml --- a/flexbar_split_RYYR_bcs.xml Mon Nov 23 10:42:04 2015 -0500 +++ b/flexbar_split_RYYR_bcs.xml Fri Nov 27 04:33:02 2015 -0500 @@ -10,7 +10,7 @@ flexbar - + flexbar --version