diff samtools_reheader.xml @ 2:77a6694ebf7a draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/samtools_reheader.xml	Fri Oct 17 14:04:50 2014 -0400
+++ b/samtools_reheader.xml	Tue Oct 13 12:55:18 2015 -0400
@@ -1,35 +1,32 @@
-<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 $2 }'</version_command>
+<tool id="samtools_reheader" name="Reheader" version="2.0">
+    <description>copy SAM/BAM header between datasets</description>
+    <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
     <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
-    <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" />
+        <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**
 
-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**
+Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
 
-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>
+    <expand macro="citations"></expand>
 </tool>