--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamsort.xml	Sat Dec 13 17:19:46 2014 -0500
@@ -0,0 +1,38 @@
+<tool id="bamsort" name="Sort BAM file">
+  <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
+  <requirements>
+    <requirement type="package" version="0.1.5">mimodd</requirement>
+  </requirements>
+  <version_command>mimodd version -q</version_command>
+  <command>
+	mimodd sort $inputfile -o $output --oformat $oformat $by_name
+  </command>
+  
+  <inputs>
+    <param name="inputfile" type="data" format="bam" label="Input file to sort" />
+    <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." />
+    <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
+  </inputs>
+  
+  <outputs>
+    <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
+      <change_format>
+	 <when input="oformat" value="sam" format="sam" />
+      </change_format>
+    </data>
+  </outputs>
+
+<help>
+.. class:: infomark
+
+   **What it does**
+
+The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.
+
+Coordinate-sorted input files are expected by most downstream MiModD tools, but note that the *SNAP Read Alignment* produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from *SNAP Read Alignment* jobs with a custom sort order.
+
+The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
+
+</help>
+</tool>
+