comparison flexbar.xml @ 27:db26fb0c6389 draft

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26:2c6ab15e5964

<!-- Flexbar tool definition for Galaxy, version 2.5 -->
<!-- Author: Johannes Roehr -->


<tool id="flexbar" name="Flexbar" version="2.5" force_history_refresh="True">
	
	<description>flexible barcode and adapter removal</description>
    
	<requirements>
        <requirement type="binary" version="2.5">flexbar</requirement>
    </requirements>
	
	<version_command>flexbar --version</version_command>
	
	<command interpreter="perl">

				--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

			--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

	</command>
	
	
	<inputs>
		
		<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
		
		
		<conditional name="cReads2">
			<param name="select" type="select" label="2nd read set (paired)">
				<option value="off" selected="true">Off</option>
				<option value="on">On</option>
			</param>
			<when value="off">
			</when>
			<when value="on">
				<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"/>
			</when>
		</conditional>
		
		
		<param name="maxUncalled" size="4" type="integer" value="0"  label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>

					<param name="select" type="select" label="Separate barcode reads">
						<option value="no" selected="true">No</option>
						<option value="yes">Yes</option>
					</param>
					<when value="yes">
						<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
					</when>
					<when value="no">
						<param name="bKeep" type="select" label="Remove barcodes within reads">
							<option value="" selected="true">Yes</option>
							<option value="--barcode-keep">No</option>

	
	<help>

**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

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27:db26fb0c6389

<!-- Flexbar tool definition for Galaxy, version 2.7 -->
<!-- Author: Johannes Roehr -->


<tool id="flexbar" name="Flexbar" version="2.7" force_history_refresh="True">
	
	<description>flexible barcode and adapter removal</description>
    
	<requirements>
        <requirement type="binary" version="2.7">flexbar</requirement>
    </requirements>
	
	<version_command>flexbar --version</version_command>
	
	<command interpreter="perl">

				--reads2 $cReads2.reads2
			#end if
		#end if
		
		#if $reads.ext == "fastqsanger":
			--qtrim-format sanger
		#end if
		#if $reads.ext == "fastqsolexa":
			--qtrim-format solexa
		#end if
		#if $reads.ext == "fastqillumina":
			--qtrim-format i1.3
		#end if
		
		
		--max-uncalled $maxUncalled
		--min-read-length $minReadLen

			--pre-trim-left $trimEnds.trimLeft
			--pre-trim-right $trimEnds.trimRight
		#end if
		
		#if $cTrimPhred.select == "on":
			--qtrim TAIL --qtrim-threshold $cTrimPhred.trimPhred
		#end if
		
		#if $cTrimLen.select == "on":
			--post-trim-length $cTrimLen.trimLen
		#end if

	</command>
	
	
	<inputs>
		
		<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data" label="Sequencing reads" optional="false"/>
		
		
		<conditional name="cReads2">
			<param name="select" type="select" label="2nd read set (paired)">
				<option value="off" selected="true">Off</option>
				<option value="on">On</option>
			</param>
			<when value="off">
			</when>
			<when value="on">
				<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
			</when>
		</conditional>
		
		
		<param name="maxUncalled" size="4" type="integer" value="0"  label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>

					<param name="select" type="select" label="Separate barcode reads">
						<option value="no" selected="true">No</option>
						<option value="yes">Yes</option>
					</param>
					<when value="yes">
						<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
					</when>
					<when value="no">
						<param name="bKeep" type="select" label="Remove barcodes within reads">
							<option value="" selected="true">Yes</option>
							<option value="--barcode-keep">No</option>

	
	<help>

**Description**

Flexbar processes 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 as well as transcriptome assemblies. It supports next-generation sequencing data in fasta and fastq format, e.g. from Roche 454 and the Illumina platform. Flexbar is available on the project_ page.

.. _project: https://github.com/seqan/flexbar

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