--- a/fpocket.xml	Tue Jul 28 08:29:23 2020 -0400
+++ b/fpocket.xml	Fri Sep 10 08:20:08 2021 +0000
@@ -1,55 +1,32 @@
 <tool id="fpocket" name="fpocket" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>- find potential binding sites in protein structures</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.1.4.2</token>
+        <import>macros.xml</import>
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
-    <description>- find potential binding sites in protein structures</description>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">fpocket</requirement>
-    </requirements>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
         ln -s '$input' ./input.pdb &&
         fpocket
             -f ./input.pdb
             #if $inp.pocket_type == 'channel':
-                -m 2.8 -M 5.5 -i 30
+                --min_alpha_size 2.8 --max_alpha_size 5.5 --min_spheres_per_pocket 30
             #elif $inp.pocket_type == 'external':
-                -m 3.5 -M 10 -i 30
+                --min_alpha_size 3.5 --max_alpha_size 10 --min_spheres_per_pocket 30
             #elif $inp.pocket_type == 'custom':
-                -m $inp.min -M $inp.max -i $inp.i -D $inp.D -C $inp.C -e $inp.e
+                --min_alpha_size $inp.min
+                --max_alpha_size $inp.max
+                --min_spheres_per_pocket $inp.i
+                --clustering_distance $inp.D
+                --clustering_method $inp.C
+                --clustering_measure $inp.e
             #end if
 
     ]]></command>
     <inputs>
         <param name="input" type="data" format="pdb" label="Input file" help="Protein structure file (PDB) to search."/>
-        <conditional name="inp">
-            <param name="pocket_type" type="select" label="Type of pocket to detect" help="Search for different kinds of pockets - or select 'custom' for more fine-grained control">
-                <option value="small_mol">Small molecule binding sites</option>
-                <option value="channel">Putative channels and small cavities</option>
-                <option value="external">Large, external pockets</option>
-                <option value="custom">Custom options (advanced)</option>
-            </param>
-            <when value="custom">
-                <param name="min" type="float" value="3" min="0" max="10" label="Minimum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/>
-                <param name="max" type="float" value="6" min="0" max="10" label="Maximum radius for an alpha sphere (angstroms)" help="An alpha sphere is an empty sphere in contact with 4 atoms in 3D space."/>
-                <param name="i" type="integer" value="35" min="20" max="50" label="Minimum number of alpha spheres a pocket must contain" help="Below this threshold pockets will not be listed in results"/>
-                <param name="D" type="float" value="2.4" min="0" max="10" label="Distance threshold for clustering algorithm (angstroms)" help="Alpha spheres may be clustered if they are separated by less than this distance"/>
-                <param name="C" type="select" value="s" label="Clustering method for grouping Voronoi vertices" help="Method for clustering alpha spheres">
-                    <option value="s">Single linkage clustering</option>
-                    <option value="m">Complete linkage clustering</option>
-                    <option value="a">Average linkage clustering</option>
-                    <option value="c">Centroid linkage clustering</option>
-                </param>
-                <param name="e" type="select" value="e" label="Distance measure for clustering">
-                    <option value="e">Euclidean distance</option>
-                    <option value="b">Manhattan distance</option>
-                </param>
-            </when>
-            <when value="small_mol"/>
-            <when value="channel"/>
-            <when value="external"/>
-        </conditional>
+        <expand macro="inputs" />
         <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
             <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
             <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
@@ -84,8 +61,8 @@
         <test>
             <param name="input" ftype="pdb" value="2brc.pdb"/>
             <param name='pocket_type' value='custom' />
-            <param name="min" value="4.0"/>
-            <param name="max" value="7.0"/>
+            <param name="min" value="1.0"/>
+            <param name="max" value="3.0"/>
             <param name="i" value="20" />
             <param name="D" value="2.0"/>
             <param name="C" value="c" />
@@ -145,8 +122,5 @@
 - A text file listing properties of all pockets detected.
 
     ]]></help>
-    <citations>
-        <citation type="doi">10.1186/1471-2105-10-168</citation>
-        <citation type="doi">10.1093/nar/gkq383</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>