--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sortBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,56 @@
+<tool id="bedtools_sortbed" name="Sort BED files" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        sortBed 
+            -i $input 
+            $option 
+            > $output
+]]>
+    </command>
+    <inputs>
+        <param format="bed" name="input" type="data" label="Sort the following BED file"/>
+        <param name="option" type="select" label="Sort by">
+            <!-- sort -k 1,1 -k2,2 -n a.bed -->
+            <option value="">chromosome, then by start position (asc)</option>
+            <option value="-sizeA">feature size in ascending order.</option>
+            <option value="-sizeD">feature size in descending order.</option>
+            <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
+            <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
+            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
+            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sortBed1.bed" ftype="bed" />
+            <param name="option" value="" />
+            <output name="output" file="sortBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Sorts a feature file by chromosome and other criteria.
+
+
+.. class:: warningmark
+
+It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
+will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
+by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>