| Previous changeset 6:c0c9b43670d0 (2012-12-30) Next changeset 8:f3b45062843e (2012-12-30) |
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Commit message:
Uploaded Flexbar galaxy tool definition file flexbar.xml |
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added:
flexbar.xml |
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| 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 |
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| b'@@ -0,0 +1,398 @@\n+\n+<!-- Author: Johannes T. Roehr -->\n+\n+<tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True">\n+\n+\t<description>flexible barcode and adapter removal</description>\n+ \n+\t<requirements>\n+ <requirement type="binary" version="2.3">flexbar</requirement>\n+ </requirements>\n+\t\n+\t<version_command>flexbar --version</version_command>\n+\t\n+\t<command interpreter="perl">\n+\t\t\n+\t\tflexbar.pl flexbar\n+\t\t\n+\t\t--threads 1\n+\t\t\n+\t\t--reads $reads\n+\t\t\n+\t\t#if $cReads2.select == "on":\n+\t\t\t#if $cReads2.reads2.ext == $reads.ext:\n+\t\t\t\t--reads2 $cReads2.reads2\n+\t\t\t#end if\n+\t\t#end if\n+\t\t\n+\t\t\n+\t\t#if $reads.ext == "fasta":\n+\t\t\t--format fasta\n+\t\t#end if\n+\t\t#if $reads.ext == "fastq":\n+\t\t\t--format fastq\n+\t\t#end if\n+\t\t#if $reads.ext == "fastqsanger":\n+\t\t\t--format fastq-sanger\n+\t\t#end if\n+\t\t#if $reads.ext == "fastqsolexa":\n+\t\t\t--format fastq-solexa\n+\t\t#end if\n+\t\t#if $reads.ext == "fastqillumina":\n+\t\t\t--format fastq-i1.3\n+\t\t#end if\n+\t\t#if $reads.ext == "csfasta":\n+\t\t\t--format csfasta\n+\t\t#end if\n+\t\t#if $reads.ext == "fastqcssanger":\n+\t\t\t--format csfastq\n+\t\t#end if\n+\t\t\n+\t\t\n+\t\t--max-uncalled $maxUncalled\n+\t\t--min-readlength $minReadLen\n+\t\t\n+\t\t#if $trimEnds.select == "on":\n+\t\t\t--pre-trim-left $trimEnds.trimLeft\n+\t\t\t--pre-trim-right $trimEnds.trimRight\n+\t\t#end if\n+\t\t\n+\t\t#if $cTrimPhred.select == "on":\n+\t\t\t--pre-trim-phred $cTrimPhred.trimPhred\n+\t\t#end if\n+\t\t\n+\t\t#if $cTrimLen.select == "on":\n+\t\t\t--post-trim-length $cTrimLen.trimLen\n+\t\t#end if\n+\t\t\n+\t\t\n+\t\t#if $cBarcodes.select == "on":\n+\t\t\t--barcodes $cBarcodes.barcodes\n+\t\t\t\n+\t\t\t#if $cBarcodes.cbReads.select == "yes":\n+\t\t\t\t--barcode-reads $cBarcodes.cbReads.bReads\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t#if $cBarcodes.cbReads.select == "no":\n+\t\t\t\t$cBarcodes.cbReads.bKeep\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t--barcode-trim-end $cBarcodes.bTrimEnd\n+\t\t\t\n+\t\t\t#if $cBarcodes.cbTailLen.select == "yes":\n+\t\t\t\t--barcode-tail-length $cBarcodes.cbTailLen.bTailLen\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t#if $cBarcodes.cbMinOverlap.select == "yes":\n+\t\t\t\t--barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t--barcode-threshold $cBarcodes.bThresh\n+\t\t\t\n+\t\t\t#if $cBarcodes.cbAlignScores.select == "yes":\n+\t\t\t\t--barcode-match $bMatch\n+\t\t\t\t--barcode-mismatch $bMismatch\n+\t\t\t\t--barcode-gap $bGap\n+\t\t\t#end if\n+\t\t\t\n+\t\t#end if\n+\t\t\n+\t\t\n+\t\t#if $cAdapters.select == "yes":\n+\t\t\t\n+\t\t\t#if $cAdapters.ccAdapters.select == "data":\n+\t\t\t\t--adapters $cAdapters.ccAdapters.adaptersData\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t#if $cAdapters.ccAdapters.select == "seq":\n+\t\t\t\t--adapter-seq $cAdapters.ccAdapters.adapterSeq\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t--adapter-trim-end $cAdapters.aTrimEnd\n+\t\t\t\n+\t\t\t#if $cAdapters.caTailLen.select == "yes":\n+\t\t\t\t--adapter-tail-length $cAdapters.caTailLen.aTailLen\n+\t\t\t#end if\n+\t\t\t\n+\t\t\t--adapter-min-overlap $cAdapters.aMinOverlap\n+\t\t\t--adapter-threshold $cAdapters.aThresh\n+\t\t\t\n+\t\t\t#if $cAdapters.caAlignScores.select == "on":\n+\t\t\t\t--adapter-match $aMatch\n+\t\t\t\t--adapter-mismatch $aMismatch\n+\t\t\t\t--adapter-gap $aGap\n+\t\t\t#end if\n+\t\t\t\n+\t\t#end if\n+\t\t\n+\t\t\n+\t\t#if $cLogging.select == "show"\n+\t\t\t$cLogging.logLevel\n+\t\t\t$cLogging.noLenDist\n+\t\t\t$cLogging.remTag\n+\t\t#end if\n+\t\t\n+\t\t#if $cLogging.select == "off"\n+\t\t\t--no-length-dist\n+\t\t#end if\n+\t\t\n+\t\t\n+\t\t$output $output.id $__new_file_path__ $reads.ext\n+\t\t\n+\t</command>\n+\t\n+\t<inputs>\n+\t\t\n+\t\t<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>\n+\t\t\n+\t\t\n+\t\t<conditional name="cReads2">\n+\t\t\t<param name="select" type="select" label="2nd read set (paired)">\n+\t\t\t\t<option value="off" selected="true">Off</option>\n+\t\t\t\t<option value="on">On</option>\n+\t\t\t</param>\n+\t\t\t<when value="on">\n+\t\t\t\t<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>\n+\t\t\t</when>\n+\t\t</conditional>\n+\t\t\n+\t\t\n+\t\t<param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optio'..b'="yes">\n+\t\t\t\t\t\t<param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>\n+\t\t\t\t\t</when>\n+\t\t\t\t</conditional>\n+\t\t\t\t\n+\t\t\t\t<param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>\n+\t\t\t\t<param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>\n+\t\t\t\t\n+\t\t\t\t<conditional name="caAlignScores">\n+\t\t\t\t\t<param name="select" type="select" label="Modify alignment scores">\n+\t\t\t\t\t\t<option value="no" selected="true">No</option>\n+\t\t\t\t\t\t<option value="yes">Yes</option>\n+\t\t\t\t\t</param>\n+\t\t\t\t\t<when value="yes">\n+\t\t\t\t\t\t<param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>\n+\t\t\t\t\t\t<param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>\n+\t\t\t\t\t\t<param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>\n+\t\t\t\t\t</when>\n+\t\t\t\t</conditional>\n+\t\t\t</when>\n+\t\t</conditional>\n+\t\t\n+\t\t\n+\t\t<conditional name="cTrimLen">\n+\t\t\t<param name="select" type="select" label="6) Trimming to length">\n+\t\t\t\t<option value="off" selected="true">Off</option>\n+\t\t\t\t<option value="on">On</option>\n+\t\t\t</param>\n+\t\t\t<when value="on">\n+\t\t\t\t<param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>\n+\t\t\t</when>\n+\t\t</conditional>\n+\t\t\n+\t\t<param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>\n+\t\t\n+\t\t\n+\t\t<conditional name="cLogging">\n+\t\t\t<param name="select" type="select" label="Logging and tagging options">\n+\t\t\t\t<option value="off" selected="true">Off</option>\n+\t\t\t\t<option value="show">Show</option>\n+\t\t\t</param>\n+\t\t\t<when value="show">\n+\t\t\t\t<param name="logLevel" type="select" label="Alignment logging">\n+\t\t\t\t\t<option value="" selected="true">Off</option>\n+\t\t\t\t\t<option value="--log-level ALL">All</option>\n+\t\t\t\t\t<option value="--log-level MOD">Modified</option>\n+\t\t\t\t\t<option value="--log-level TAB">Tabular</option>\n+\t\t\t\t</param>\n+\t\t\t\n+\t\t\t\t<param name="noLenDist" type="select" label="Read length distribution">\n+\t\t\t\t\t<option value="--no-length-dist" selected="true">Off</option>\n+\t\t\t\t\t<option value="">On</option>\n+\t\t\t\t</param>\n+\t\t\n+\t\t\t\t<param name="remTag" type="select" label="Read tagging">\n+\t\t\t\t\t<option value="" selected="true">Off</option>\n+\t\t\t\t\t<option value="--removal-tag">Removal tags</option>\n+\t\t\t\t</param>\n+\t\t\t</when>\n+\t\t</conditional>\n+\n+ \t</inputs>\n+ \t\n+\t<stdio>\n+\t <exit_code range="1:" level="fatal" description="Error!" />\n+\t</stdio>\n+\t\n+\t<outputs>\n+\t <data format="txt" name="output" metadata_source="reads"/>\n+\t </outputs>\n+\t\n+\t\n+\t<help>\n+**Flexbar help**\n+\n+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.\n+\n+.. _Flexbar: https://sourceforge.net/projects/flexbar\n+\n+------\n+\n+**Reference**\n+\n+Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar \xe2\x80\x94 flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.\n+\n+------\n+\n+**Trim-end modes**\n+\n+**Any:** longer part of read remains\n+\n+**Left:** align before or at read end, right part remains\n+\n+**Right:** align after or at read start, left part remains\n+\n+**Left tail:** consider first n bases, see tail-length options\n+\n+**Right tail:** use only last n bases of reads in alignment\n+\n+------\n+\n+**Documentation**\n+\n+.. class:: warningmark\n+\n+Further documentation is available on the `manual`__ wiki and via the command line help screen.\n+\n+.. __: http://sourceforge.net/p/flexbar/wiki\n+\t</help>\n+\n+</tool>\n+\n' |