diff reheader.xml @ 0:7da2c9654a83 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reheader.xml	Tue Aug 12 11:26:15 2014 -0400
@@ -0,0 +1,33 @@
+<tool id="reheader" name="Reheader BAM file">
+  <description>From a BAM file generate a new file with the original header (if any) replaced by that found in a second SAM file</description>
+  <requirements>
+    <requirement type="package" version="3.4.1">python3</requirement>
+    <requirement type="package" version="0.1.3_9af04e0e9125">MiModD</requirement>
+  </requirements>
+  <command>
+	mimodd reheader $template $input -o $output --verbose
+  </command>
+  
+  <inputs>
+    <param name="input" type="data" format="bam" label="Input file in BAM format" help="The file to reheader." />
+    <param name="template" type="data" format="sam" label="Header template file in SAM format" help="Use the header information of this file" />
+  </inputs>
+  
+  <outputs>
+    <data name="output" format="bam" label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}">
+    </data>
+  </outputs>
+
+<help>
+.. class:: infomark
+
+   **What it does**
+
+The tool replaces the header of the input BAM file (i.e., its metadata) with that found in the template SAM file and writes the result to a new BAM file.
+
+Typically, you will generate the header template file with the *NGS Run Annotation* tool, but any SAM file with header information can be used instead.
+
+</help>
+
+</tool>
+