--- a/get_flanks.xml	Wed Nov 11 12:48:31 2015 -0500
+++ b/get_flanks.xml	Thu Jun 22 18:41:29 2017 -0400
@@ -1,57 +1,62 @@
 <tool id="get_flanks1" name="Get flanks" version="1.0.0">
-  <description>returns flanking region/s for every gene</description>
-  <requirements>
-    <requirement type="package" version="0.7.1">bx-python</requirement>
-    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
-  </requirements>
-  <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
-  <inputs>
-    <param format="interval" name="input" type="data" label="Select data"/>
-    <param name="region" type="select" label="Region">
-      <option value="whole" selected="true">Whole feature</option>
-      <option value="start">Around Start</option>
-      <option value="end">Around End</option>
-    </param>
-    <param name="direction" type="select" label="Location of the flanking region/s">
-      <option value="Upstream">Upstream</option>
-      <option value="Downstream">Downstream</option>
-      <option value="Both">Both</option>
-    </param>
-    <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
-    <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
-    
-    
-  </inputs>
-  <outputs>
-    <data format="interval" name="out_file1" metadata_source="input"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="flanks_inp.bed"/>
-      <param name="offset" value="-500"/>
-      <param name="size" value="1000"/>
-      <param name="direction" value="Both"/>
-      <param name="region" value="whole"/>
-      <output name="out_file1" file="flanks_out1.bed"/>
-    </test>
-    <test>
-      <param name="input" value="flanks_inp.bed"/>
-      <param name="offset" value="200"/>
-      <param name="size" value="1000"/>
-      <param name="direction" value="Downstream"/>
-      <param name="region" value="start" />
-      <output name="out_file1" file="flanks_out2.bed"/>
-    </test>
-  </tests>
- <help> 
-
-This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. 
+    <description>returns flanking region/s for every gene</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+python '$__tool_directory__/get_flanks.py'
+'$input'
+'$out_file1'
+$size
+$direction
+$region
+-o $offset
+-l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="interval" label="Select data"/>
+        <param name="region" type="select" label="Region">
+            <option value="whole" selected="true">Whole feature</option>
+            <option value="start">Around Start</option>
+            <option value="end">Around End</option>
+        </param>
+        <param name="direction" type="select" label="Location of the flanking region/s">
+            <option value="Upstream">Upstream</option>
+            <option value="Downstream">Downstream</option>
+            <option value="Both">Both</option>
+        </param>
+        <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
+        <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="input" metadata_source="input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="flanks_inp.bed"/>
+            <param name="offset" value="-500"/>
+            <param name="size" value="1000"/>
+            <param name="direction" value="Both"/>
+            <param name="region" value="whole"/>
+            <output name="out_file1" file="flanks_out1.bed"/>
+        </test>
+        <test>
+            <param name="input" value="flanks_inp.bed"/>
+            <param name="offset" value="200"/>
+            <param name="size" value="1000"/>
+            <param name="direction" value="Downstream"/>
+            <param name="region" value="start" />
+            <output name="out_file1" file="flanks_out2.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
 
 **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
 
 -----
 
-
 **Example 1**
 
 - For the following dataset::
@@ -75,8 +80,5 @@
    chr22  500  800  NM_028946 0 -
 
 .. image:: flanks_ex2.gif
-
-</help>  
-
-
+    ]]></help>
 </tool>