--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rbcavity.xml	Sat Apr 04 15:04:13 2020 -0400
@@ -0,0 +1,93 @@
+<tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1">
+    <description>- generate the active site definition needed for rxDock docking</description>
+    <macros>
+        <import>rdock_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        ln -s '$receptor_prm' receptor.prm &&
+        ln -s '$receptor' receptor.mol2 &&
+        ln -s '$ligand' ligand.sdf &&
+        rbcavity -W -d -r receptor.prm &&
+        ls -l
+    ]]></command>
+
+    <configfiles>
+        <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
+RECEPTOR_FILE receptor.mol2
+RECEPTOR_FLEX 3.0
+SECTION MAPPER
+    SITE_MAPPER RbtLigandSiteMapper
+    REF_MOL ligand.sdf
+    RADIUS $radius
+    SMALL_SPHERE $sphere
+    MIN_VOLUME $min_volume
+    MAX_CAVITIES 1
+    VOL_INCR $vol_incr
+    GRIDSTEP $gridstep
+END_SECTION
+SECTION CAVITY
+    SCORING_FUNCTION RbtCavityGridSF
+    WEIGHT $weight
+END_SECTION
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (Mol2 format)."/>
+        <param type="data" name="ligand" format="mol,sdf" label="Reference ligand" help="Single ligand in Mol or SDF format"/>
+        <param name="radius" type="float" value="6.0" min="0" label="Mapper sphere radius"
+            help="Mapper radius of large sphere in angstroms; rxDock will search for cavities to the small sphere but not to the large sphere"/>
+        <param name="sphere" type="float" value="1.0" min="0" label="Mapper small sphere radius"
+            help="Mapper radius of small sphere in angstroms; rxDock will search for cavities accessible to the small sphere but not to the large sphere"/>
+        <param name="min_volume" type="integer" value="100" min="0" label="Mapper minimum volume"
+            help="Mapper minimum volume in cubic angstroms. rxDock will ignore cavities which are smaller than this value"/>
+        <param name="vol_incr" type="float" value="0.0" min="0" label="Mapper volume increment"
+            help="Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rxDock will temporarily increase the radius of receptor atoms by this amount"/>
+        <param name="gridstep" type="float" value="0.5" min="0" label="Mapper grid step" help="Grid resolution for mapping in angstroms"/>
+        <param name="weight" type="float" value="1.0" min="0" label="Cavity weight" help="Cavity weight"/>
+    </inputs>
+    <outputs>
+        <data name="activesite" format="rdock_as" from_work_dir="receptor.as" label="rbcavity active site on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="receptor" value="receptor.mol2"/>
+            <param name="ligand" value="ligand.sdf"/>
+            <output name="activesite" file="receptor.as" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="receptor" value="receptor.mol2"/>
+            <param name="ligand" value="ligand.mol"/>
+            <output name="activesite" file="receptor.as" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+This tool generates the cavity definition for rxDock docking (the receptor.as file) using the rbcavity program.
+See https://www.rxdock.org for more details about rxDock and associated programs.
+Only a subset of the parameters are currently exposed. Read the rxDock docs for a full understanding.
+
+-----
+
+.. class:: infomark
+
+**Inputs**
+
+1. The protein receptor to dock into as a file in Mol2 format.
+2. A reference ligand used to define the location of the active site in Molfile or SDF format.
+3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all.
+
+-----
+
+.. class:: infomark
+
+**Outputs**
+
+An active site definition binary file (receptor.as) that is needed by the rxDock docking program to guide the docking.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>