# HG changeset patch
# User devteam
# Date 1413569027 14400
# Node ID c50efc142ad09fa3eb5116628a0eaf4d7aacda53

Uploaded initial tool definition.

diff -r 000000000000 -r c50efc142ad0 samtools_reheader.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_reheader.xml	Fri Oct 17 14:03:47 2014 -0400
@@ -0,0 +1,35 @@
+<tool id="samtools_reheader" name="Replace header" version="1.0.0">
+    <description>on a BAM or SAM file</description>
+    <requirements>
+        <requirement type="package" version="1.1">samtools</requirement>
+    </requirements>
+    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <inputs>
+        <param name="input_header" type="data" format="sam" label="SAM file or header" />
+        <param name="input_file" type="data" format="sam,bam" label="File to reheader" />
+    </inputs>
+    <outputs>
+        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+**What it does**
+
+This tool runs the ``samtools reheader`` command in the SAMtools toolkit.
+
+Replace the header for a SAM or BAM file with a different header.
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+    </help>
+</tool>
+
diff -r 000000000000 -r c50efc142ad0 test-data/phiX.bam
Binary file test-data/phiX.bam has changed
diff -r 000000000000 -r c50efc142ad0 test-data/samtools_reheader_in1.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_reheader_in1.sam	Fri Oct 17 14:03:47 2014 -0400
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:phiX174	LN:5386
+@PG	ID:bowtie2	PN:bowtie2	VN:2.1.0
diff -r 000000000000 -r c50efc142ad0 test-data/samtools_reheader_in2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_reheader_in2.sam	Fri Oct 17 14:03:47 2014 -0400
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:phiX174	LN:5386
+@PG	ID:manual	PN:vim	VN:7.4.52
diff -r 000000000000 -r c50efc142ad0 test-data/samtools_reheader_out1.bam
Binary file test-data/samtools_reheader_out1.bam has changed
diff -r 000000000000 -r c50efc142ad0 test-data/samtools_reheader_out2.bam
Binary file test-data/samtools_reheader_out2.bam has changed
diff -r 000000000000 -r c50efc142ad0 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 17 14:03:47 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>