diff samtools_reheader.xml @ 0:020e144b5f78 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_reheader.xml	Tue Apr 21 16:57:10 2015 -0400
@@ -0,0 +1,32 @@
+<tool id="samtools_reheader" name="Reheader" version="2.0">
+    <description>copy SAM/BAM header between datasets</description>
+    <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
+    <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
+    <inputs>
+        <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
+        <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
+    </inputs>
+    <outputs>
+        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
+            <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
+            <output name="output" ftype="bam" file="reheader_out.bam"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
+
+    </help>
+    <expand macro="citations"></expand>
+</tool>
+