--- a/prepare_box.xml	Wed Oct 02 12:49:11 2019 -0400
+++ b/prepare_box.xml	Fri Oct 18 04:57:34 2019 -0400
@@ -1,12 +1,13 @@
-<tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.0">
-    <description>job from an input mol file (confounding box)</description>
+<tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.1">
+    <description>job from a ligand input file (confounding box)</description>
     <requirements>
-        <requirement type="package" version="2019.03.1.0">rdkit</requirement>
+        <requirement type="package" version="2019.03.1">rdkit</requirement>
         <requirement type="package" version="1.16.2">numpy</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python '$__tool_directory__/calc_vina_box_params.py'
         --ligand '$ligand'
+        --ftype '${ligand.ext}'
         --config '$output'
         --bufx '$bufx'
         --bufy '$bufy'
@@ -19,8 +20,8 @@
         #end if
     ]]></command>
     <inputs>
-        <param type="data" name="ligand" format="mol" label="Input ligand"
-            help="The input ligand (mol file)"/>
+        <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand"
+            help="The input ligand with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
         <param name="bufx" type="float" value="0" label="x-axis buffer"
             help="Buffer in the x direction (in angs.)"/>
         <param name="bufy" type="float" value="0" label="y-axis buffer"
@@ -37,14 +38,30 @@
     </outputs>
     <tests>
         <test>
-            <param name="ligand" value="NUDT5A-x0114_2.mol" />
+            <param name="ligand" value="NUDT5A-x0114_2.mol" ftype="mol"/>
             <param name="bufx" value="1" />
             <param name="bufy" value="2" />
             <param name="bufz" value="3" />
             <output name="output" file="box_params_1.txt" />
         </test>
         <test>
-            <param name="ligand" value="NUDT5A-x0114_2.mol" />
+            <param name="ligand" value="NUDT5A-x0114_2.sdf" ftype="sdf"/>
+            <param name="bufx" value="1" />
+            <param name="bufy" value="2" />
+            <param name="bufz" value="3" />
+            <param name="exh" value="10" />
+            <param name="seed_value" value="1" />
+            <output name="output" file="box_params_2.txt" />
+        </test>
+        <test>
+            <param name="ligand" value="NUDT5A-x0114_2.mol2"/>
+            <param name="bufx" value="1" />
+            <param name="bufy" value="2" />
+            <param name="bufz" value="3" />
+            <output name="output" file="box_params_1.txt" />
+        </test>
+        <test>
+            <param name="ligand" value="NUDT5A-x0114_2.pdb" ftype="pdb"/>
             <param name="bufx" value="1" />
             <param name="bufy" value="2" />
             <param name="bufz" value="3" />
@@ -60,10 +77,10 @@
 
 **Description**
 
-This tool calculates a confounding box around an input ligand (mol file), and
+This tool calculates a confounding box around an input ligand and
 uses it to generate the input parameters for an autodock vina job.
 
-The output file can be fed into the autodock vina tool as an alternative to creating the
+The output file can be fed into the AutoDock Vina tool as an alternative to creating the
 parameter file manually.
 
 -----
@@ -74,7 +91,7 @@
 
 This tool requires:
 
-* An input ligand - This should be a mol file representing the ligand you wish to dock. This should be derived from the file you use to prepare the ligand for the docking job (see prepare ligand tool).
+* An input ligand - This should be a file (MOL, SDF, PDB or MOL2 format) representing the ligand you wish to dock.
 
 * (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore.