--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare_box.xml	Wed Apr 17 09:11:01 2019 -0400
@@ -0,0 +1,102 @@
+<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>
+    <requirements>
+        <requirement type="package" version="2019.03.1.0">rdkit</requirement>
+        <requirement type="package" version="1.16.2">numpy</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/calc_vina_box_params.py'
+        --ligand '$input1'
+        --config '$output1'
+        --bufx '$bufx'
+        --bufy '$bufy'
+        --bufz '$bufz'
+        --exh '$exh'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="mol" label="input ligand mol file"
+            help="The input ligand (mol file)"/>
+        <param name="bufx" type="float" value="0" label="x-axis buffer"
+            help="the buffer in the x direction (in angs.)"/>
+        <param name="bufy" type="float" value="0" label="y-axis buffer"
+            help="the buffer in the y direction (in angs.)"/>
+        <param name="bufz" type="float" value="0" label="z-axis buffer"
+            help="the buffer in the z direction (in angs.)"/>
+        <param name="exh" type="integer" value="0" label="exhaustiveness"
+            help="The number of poses to return from docking job"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="NUDT5A-x0114_2.mol" />
+            <param name="bufx" value="1" />
+            <param name="bufy" value="2" />
+            <param name="bufz" value="3" />
+            <param name="exh" value="10" />
+            <output name="output1" file="box_params.txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Description:**
+
+This tool calculates a confounding box around an input ligand (mol file), 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
+parameter file manually.
+
+-----
+.. class:: infomark
+
+**Inputs:**
+
+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).
+
+* OPTIONAL Buffers for each direction (x,y,z), which defaults to 0 angstroms. 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.
+
+-----
+.. class:: infomark
+
+**Output:**
+
+The output for this tool is a txt file containing the parameters needed to run an autodock
+vina docking calculation with the docking tool. For example:
+
+size_x =  12.443000000000001
+size_y =  11.888
+size_z =  9.290999999999997
+center_x =  -29.8395
+center_y =  4.364
+center_z =  -64.5925
+num_modes = 9999
+energy_range = 9999
+exhaustiveness = 10
+cpu = 4
+seed = 1
+
+The values for num_modes, energy range, cpu and seed are set to default values here.
+
+This file can be used as the box parameter for the docking tool.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @article{rdkit,
+                author = {Greg Landrum},
+                title = {RDKit: Open-source cheminformatics},
+                url ={http://www.rdkit.org}
+            }</citation>
+    </citations>
+</tool>