Mercurial > repos > yhoogstrate > samtools_view_header

<?xml version="1.0" encoding="UTF-8"?>
<tool id="samtools_view_header" name="Samtools view header" version="0.1.19.a">
	<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>

	<version_command>samtools 2&gt;&amp;1 | grep -i "version:"</version_command>

	<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="Alignment in BAM or SAM format" />
	</inputs>

	<outputs>
		<data format="tabular" name="header" label="${tool.name} on ${alignment.name}" />
	</outputs>

	<help>
**samtools_view_header**

**Input formats**

* BAM
* SAM

**Output format**

The SAM header as defined in the SAM specification. If the output is empty, there was no header in the alignment


**Installation**

The installation is straight-forward and should go automatically using the Galaxy tool-shed installer.

**License**

* samtools: MIT License

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 toolsheds:

http://toolshed.dtls.nl/

http://toolshed.g2.bx.psu.edu

http://testtoolshed.g2.bx.psu.edu/
</help>
</tool>
author	yhoogstrate
date	Thu, 20 Nov 2014 03:55:28 -0500
parents	1a77794c72ed
children