--- a/groupbyBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/groupbyBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,23 +6,31 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools groupby
-        -c $cols
+        -c "${cols}"
         -g $group
         -o $operation
-        -i $inputA
-        &gt; $output
+        -i "${inputA}"
+        > "${output}"
+]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" />
-        <param name="group" type="text" value="1,2,3" label="Specifies which column(s) (1-based) should be used to group the input. Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed." />
-        <param name="operation" type="select" label="Specify the operation">
+        <param format="bed" name="inputA" type="data" label="BED file"/>
+        <expand macro="choose_columns" />
+        <param name="group" type="text" value="1,2,3" 
+            label="Specifies which column(s) (1-based) should be used to group the input"
+            help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits"><add value=","/><add value="-"/></valid>
+            </sanitizer>
+        </param>
+        <param name="operation" type="select" label="Specify the operation" help="(-o)">
             <option value="sum" selected="True">Sum - numeric only</option>
             <option value="stdev">Stdev - numeric only</option>
             <option value="sstdev">Sstdev - numeric only</option>
-            <option value="freqasc">Freqasc - print a comma separated list of values observed and the number of times they were observed. Reported in ascending order of frequency*</option>
-            <option value="freqdesc">Freqdesc - - print a comma separated list of values observed and the number of times they were observed. Reported in descending order of frequency*</option>
+            <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
+            <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
             <option value="first">First - numeric or text</option>
             <option value="last">Last - numeric or text</option>
             <expand macro="math_options" />
@@ -30,15 +38,39 @@
         </param>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+        <data format_source="inputA" name="output" metadata_source="inputA"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
+            <param name="cols" value="9" />
+            <param name="group" value="1,2,3" />
+            <param name="operation" value="sum" />
+            <output name="output" file="groupbyBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
+            <param name="cols" value="9" />
+            <param name="group" value="1,2,3" />
+            <param name="operation" value="min" />
+            <output name="output" file="groupbyBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
+            <param name="cols" value="9" />
+            <param name="group" value="1-4" />
+            <param name="operation" value="median" />
+            <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 Replicate lines in a file based on columns of comma-separated values.
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>