diff sortBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- a/sortBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/sortBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,7 +6,12 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
-        sortBed -i $input $option &gt; $output
+<![CDATA[
+        sortBed 
+            -i $input 
+            $option 
+            > $output
+]]>
     </command>
     <inputs>
         <param format="bed" name="input" type="data" label="Sort the following BED file"/>
@@ -21,13 +26,18 @@
             <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
         </param>
     </inputs>
-
     <outputs>
         <data format="bed" name="output" metadata_source="input" label="${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.
@@ -40,7 +50,7 @@
 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>