view samtools_view_header.xml @ 0:73429bd06e71 draft

Uploaded

<?xml version="1.0" encoding="UTF-8"?>
<tool id="samtools_view_header" name="Samtools view header">
	<description>Show only the header of a BAM or SAM file using samtools.</description>
	<requirements>
		<requirement type="package" version="5.9">ncurses</requirement>
		<requirement type="package" version="0.1.19">samtools</requirement>
	</requirements>
	<command>
		samtools
			 view 
			 -H 
			#if $alignment.dataset.ext.lower() == "sam"
			 -S
			#end if
			 $alignment > $header 2> stderr.txt ;
		
		cat stderr.txt
	</command>
	
	<inputs>
		<param format="sam,bam" name="alignment" type="data" label="Alignments in BAM or SAM format" help="The set of aligned reads." />
	</inputs>
	
	<outputs>
		<data format="tabular" name="header" label="${tool.name} on ${alignment.name}" />
	</outputs>
	
	<help>
**samtools view -H **

**Input formats**

**Installation**


**License**

* samtools: ....

**Contact**

The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch

More tools by the Translational Research IT (TraIT) project can be found in the following repository:
http://toolshed.dtls.nl/
</help>
</tool>