# HG changeset patch
# User yhoogstrate
# Date 1402489274 14400
# Node ID 73429bd06e71dc80ca2c2982bd319b4398e09db1

Uploaded

diff -r 000000000000 -r 73429bd06e71 samtools_view_header.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_view_header.xml	Wed Jun 11 08:21:14 2014 -0400
@@ -0,0 +1,48 @@
+<?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>
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diff -r 000000000000 -r 73429bd06e71 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jun 11 08:21:14 2014 -0400
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="ncurses" version="5.9">
+		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+	</package>
+		
+	<package name="samtools" version="0.1.19">
+		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+	</package>
+</tool_dependency>
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