comparison flexbar.xml @ 13:346a2b0979ea

Adjusted tool definition and wrapper to Flexbar 2.31 release.

12:4cbf6c6d2f2b

<!-- Author: Johannes T. Roehr -->

<tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True">

	<description>flexible barcode and adapter removal</description>
    
	<requirements>
        <requirement type="binary" version="2.3">flexbar</requirement>
    </requirements>
	
	<version_command>flexbar --version</version_command>
	
	<command interpreter="perl">

		#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
		

					<option value="" selected="true">Off</option>
					<option value="--log-level ALL">All</option>
					<option value="--log-level MOD">Modified</option>
					<option value="--log-level TAB">Tabular</option>
				</param>
			
				<param name="noLenDist" type="select" label="Read length distribution">
					<option value="--no-length-dist" selected="true">Off</option>
					<option value="">On</option>
				</param>
		
				<param name="remTag" type="select" label="Read tagging">
					<option value="" selected="true">Off</option>
					<option value="--removal-tag">Removal tags</option>
				</param>
			</when>
		</conditional>

  	</inputs>
 	
	<stdio>
	    <exit_code range="1:" level="fatal" description="Error!" />
	</stdio>
	
	<outputs>
	    <data format="txt" name="output" metadata_source="reads"/>
	  </outputs>
	
	
	<help>
**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**

13:346a2b0979ea

<!-- Flexbar tool definition for Galaxy, version 2.31 -->
<!-- Author: Johannes Roehr -->

<tool id="flexbar" name="Flexbar" version="2.31" force_history_refresh="True">

	<description>flexible barcode and adapter removal</description>
    
	<requirements>
        <requirement type="binary" version="2.31">flexbar</requirement>
    </requirements>
	
	<version_command>flexbar --version</version_command>
	
	<command interpreter="perl">

		#end if
		
		
		#if $cLogging.select == "show":
			$cLogging.logLevel
			$cLogging.singleReads
			$cLogging.lenDist
			$cLogging.fastaOutput
			$cLogging.numTags
			$cLogging.remTags
		#end if
		
		
		$output $output.id $__new_file_path__ $reads.ext
		

					<option value="" selected="true">Off</option>
					<option value="--log-level ALL">All</option>
					<option value="--log-level MOD">Modified</option>
					<option value="--log-level TAB">Tabular</option>
				</param>
				
				<param name="singleReads" type="select" label="Single reads">
					<option value="" selected="true">Off</option>
					<option value="--single-reads">On</option>
				</param>
				
				<param name="lenDist" type="select" label="Read length distribution">
					<option value="" selected="true">Off</option>
					<option value="--length-dist">On</option>
				</param>
				
				<param name="fastaOutput" type="select" label="Fasta output">
					<option value="" selected="true">Off</option>
					<option value="--fasta-output">Always</option>
				</param>
				
				<param name="numTags" type="select" label="Number tags">
					<option value="" selected="true">Off</option>
					<option value="--number-tags">On</option>
				</param>
				
				<param name="remTags" type="select" label="Removal tags">
					<option value="" selected="true">Off</option>
					<option value="--removal-tags">On</option>
				</param>
			</when>
		</conditional>
		
  	</inputs>
 	
	<stdio>
	    <exit_code range="1:" level="fatal" description="Error!" />
	</stdio>
	
	<outputs>
	    <data format="txt" name="output" metadata_source="reads"/>
	</outputs>
	
	
	<help>

**Flexbar description**

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

------

**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

------

**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.

------

**Documentation**