--- a/smina.xml	Wed Sep 14 09:47:48 2016 -0400
+++ b/smina.xml	Tue Sep 20 09:57:24 2016 -0400
@@ -130,24 +130,24 @@
     </command>
     <inputs>
         <section name="input" title="Input" expanded="True">
-            <param name="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/>
-            <param name="ligand" type="data" format="data" label="ligand(s)" help="(--ligand)"/>
-            <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex)"/>
-            <param name="flexres" type="text" label="flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/>
+            <param name="receptor" type="data" format="pdbqt" label="Rigid part of the receptore" help="(--receptor)"/>
+            <param name="ligand" type="data" format="data" label="Ligand(s)" help="(--ligand)"/>
+            <param name="flex" type="data" format="pdbqt" label="Flexible side chains, if any" optional="true" help="(--flex)"/>
+            <param name="flexres" type="text" label="Flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/>
             <param name="flexdist_ligand" type="data" format="data" label="Ligand to use for flexdist" optional="true" help="(--flexdist_ligand)"/>
-            <param name="flexdist" type="float" label="set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(--flexdist)"/>
+            <param name="flexdist" type="float" label="Set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(--flexdist)"/>
         </section>
         <section name="search_space" title="Search space" expanded="True">
             <param name="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/>
             <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/>
             <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/>
-            <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/>
-            <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/>
-            <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/>
+            <param name="size_x" type="integer" value="1" label="Size in the X dimension" help="(--size_x)"/>
+            <param name="size_y" type="integer" value="1" label="Size in the Y dimension" help="(--size_y)"/>
+            <param name="size_z" type="integer" value="1" label="Size in the Z dimension" help="(--size_z)"/>
 
             <param name="autobox_ligand" type="data" format="data" label="Ligand to use for autobox" optional="true" help="(--autobox_ligand)"/>
-            <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" help="(--autobox_add)"/>
-            <param name="no_lig" type="select" label="no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" help="(--no_lig)">
+            <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text" optional="true" help="(--autobox_add)"/>
+            <param name="no_lig" type="select" label="No ligand; for sampling/minimizing flexible residues " help="(--no_lig)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>
@@ -165,13 +165,13 @@
                 <option value="false" selected="true" >No </option>
                 <option value="true" >Yes </option>
             </param>
-            <param name="atom_term_data" type="select" label="embedded per-atom interaction terms in output sd data" help="(--atom_term_data)">
+            <param name="atom_term_data" type="select" label="Embedded per-atom interaction terms in output sd data" help="(--atom_term_data)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>
         </section>
         <section name="scoring_and_minimization" title="Scoring and minimization options" >
-            <param name="scoring" type="select" label="specify alternative builtin scoring function" help="(--scoring)">
+            <param name="scoring" type="select" label="Specify alternative builtin scoring function" help="(--scoring)">
                 <option value="default" selected="true">default</option>
                 <option value="ad4_scoring">ad4_scoring</option>
                 <option value="dkoes_fast">dkoes_fast</option>
@@ -180,26 +180,26 @@
                 <option value="vina">vina</option>
                 <option value="vinardo">vinardo</option>
             </param>
-            <param name="custom_scoring" type="data" format="data" label="custom scoring function file" optional="true" help="(--custom_scoring)"/>
-            <param name="custom_atoms" type="data" format="data" label="custom atom type parameters file" optional="true" help="(--custom_atoms)"/>
-            <param name="score_only" type="select" label="score provided ligand pose" help="(--score_only)">
+            <param name="custom_scoring" type="data" format="data" label="Custom scoring function file" optional="true" help="(--custom_scoring)"/>
+            <param name="custom_atoms" type="data" format="data" label="Custom atom type parameters file" optional="true" help="(--custom_atoms)"/>
+            <param name="score_only" type="select" label="Score provided ligand pose" help="(--score_only)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
                 </param>
-            <param name="local_only" type="select" label="local search only using autobox (you probably want to use --minimize)" help="(--local_only)">
+            <param name="local_only" type="select" label="Local search only using autobox" help="(--local_only)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>
-            <param name="minimize" type="select" label="energy minimization" help="(--minimize)">
+            <param name="minimize" type="select" label="Energy minimization" help="(--minimize)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>
-            <param name="randomize_only" type="select" label="generate random poses, attempting to avoid clashes" help="(--randomize_only)">
+            <param name="randomize_only" type="select" label="Generate random poses, attempting to avoid clashes" help="(--randomize_only)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>
-            <param name="minimize_iters" type="integer" value="0" label="number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" help="(--minimize_iters)"/>    
-            <param name="accurate_line" type="select" label="use accurate line search" help="(--accurate_line)">
+            <param name="minimize_iters" type="integer" value="0" label="Number iterations of steepest descent" help="(--minimize_iters)"/>    
+            <param name="accurate_line" type="select" label="Accurate line search" help="(--accurate_line)">
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>        
@@ -207,15 +207,15 @@
                 <option value="false" selected="true">Do not use this option</option>
                 <option value="true">Use this option</option>
             </param>
-            <param name="approximation" type="select" label="approximation (linear, spline, or exact) to use" optional="true" help="(--approximation)">
+            <param name="approximation" type="select" label="Approximation" optional="true" help="(--approximation)">
                 <option value="linear">linear</option>
                 <option value="spline">spline</option>
                 <option value="exact">exact</option>
             </param>
-            <param name="factor" type="float" label="approximation factor: higher results in a finer-grained approximation" optional="true" help="(--factor)">
+            <param name="factor" type="float" label="Approximation factor: higher results in a finer-grained approximation" optional="true" help="(--factor)">
                 <validator type="in_range" min="0"/>
             </param>
-            <param name="force_cap" type="float" label="max allowed force; lower values more gently minimize clashing structures" optional="true" help="(--force_cap)"/>
+            <param name="force_cap" type="float" label="Max allowed force; lower values more gently minimize clashing structures" optional="true" help="(--force_cap)"/>
             <param name="user_grid" type="float" label="Autodock map file for user grid data based calculations" optional="true" help="(--user_grid)"/>
             <param name="user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring"  help="(--user_grid_lambda)"/>
             <param name="print_terms" type="select" label="Print all available terms with default parameterizations" help="(--print_terms)">
@@ -228,15 +228,15 @@
             </param>
         </section>
         <section name="misc" title="Misc" >
-            <param name="cpu" type="integer" label="the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)" optional="true" help="(--cpu)"/>
-            <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/>
-            <param name="exhaustiveness" type="integer" value="8" label="exhaustiveness of the global search (roughly proportional to time)" help="(--exhaustiveness)"/>
-            <param name="num_modes" type="integer" value="9" label="exhaustiveness of the global search (roughly proportional to time)" help="(--num_modes)">
+            <param name="cpu" type="integer" label="The number of CPUs to use" optional="true" help="(--cpu)"/>
+            <param name="seed" type="float" label="Explicit random seed" optional="true" help="(--seed)"/>
+            <param name="exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" help="(--exhaustiveness)"/>
+            <param name="num_modes" type="integer" value="9" label="Maximum number of binding modes to generate" help="(--num_modes)">
                 <validator type="in_range" min="1"/>
             </param>
-            <param name="energy_range" type="float" value="3" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/>
-            <param name="min_rmsd_filter" type="float" value="1" label="rmsd value used to filter final poses to remove redundancy" help="(--min_rmsd_filter)"/>
-            <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)">
+            <param name="energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/>
+            <param name="min_rmsd_filter" type="float" value="1" label="Rmsd value used to filter final poses to remove redundancy" help="(--min_rmsd_filter)"/>
+            <param name="addH" type="select" label="Automatically add hydrogens in ligands" help="(--addH)">
                 <option value="false" >Do not use this option</option>
                 <option value="true" selected="true">Use this option</option>
             </param>
@@ -282,71 +282,76 @@
 ******
 Help
 ******
-
- **Input**
-
- --receptor arg                             rigid part of the receptor (PDBQT)
- --flex arg                                flexible side chains, if any (PDBQT)
- --ligand arg                              ligand(s)
- --flexres arg                             flexible side chains specified by comma separated list of chain:resid
- --flexdist_ligand arg                     Ligand to use for flexdist
- --flexdist arg          set all side chains within 
-                         specified distance to flexdist_ligand to flexible
+    **Input:**
+      --receptor arg         rigid part of the receptor (PDBQT)
+      --flex arg             flexible side chains, if any (PDBQT)
+      --ligand arg           ligand(s)
+      --flexres arg          flexible side chains specified by comma separated list 
+                             of chain:resid
+      --flexdist_ligand arg  ligand to use for flexdist
+      --flexdist arg         set all side chains within specified distance to 
+                             flexdist_ligand to flexible
+    
+    **Search space:**
+      --center_x arg        X coordinate of the center
+      --center_y arg        Y coordinate of the center
+      --center_z arg        Z coordinate of the center
+      --size_x arg          size in the X dimension (Angstroms)
+      --size_y arg          size in the Y dimension (Angstroms)
+      --size_z arg          size in the Z dimension (Angstroms)
+      --autobox_ligand arg  ligand to use for autobox
+      --autobox_add arg     amount of buffer space to add to auto-generated box 
+                            (default +4 on all six sides)
+      --no_lig              no ligand; for sampling/minimizing flexible residues
+    
+    **Output (optional):**
+      --out_flex                   write output file for flexible receptor residues
+      --log                        optionally, write log file
+      --atom_terms                 optionally write per-atom interaction term values
+      --atom_term_data             embedded per-atom interaction terms in output sd data
     
- **Search space**
-
- --center_x arg         X coordinate of the center
- --center_y arg         Y coordinate of the center
- --center_z arg         Z coordinate of the center
- --size_x arg           size in the X dimension (Angstroms)
- --size_y arg           size in the Y dimension (Angstroms)
- --size_z arg           size in the Z dimension (Angstroms)
- --autobox_ligand arg   Ligand to use for autobox
- --autobox_add arg      Amount of buffer space to add 
-                        to auto-generated box (default +4 on all six sides)
- --no_lig               no ligand; for 
-                        sampling/minimizing flexible residues
-
- **Scoring and minimization options**
-
- --scoring arg                       specify alternative
-                                     builtin scoring function
- --custom_scoring arg                 custom scoring function file
- --custom_atoms arg           custom atom type parameters file
- --score_only                 score provided ligand pose
- --local_only                 local search only using autobox (you probably want to use --minimize)
- --minimize                   energy minimization
- --randomize_only             generate random poses, attempting to avoid clashes
- --minimize_iters arg         number iterations of steepest descent; 
-                              default scales with rotors and usually isn't
-                              sufficient for convergence
- --accurate_line              use accurate line search  
- --minimize_early_term        Stop minimization before convergence conditions are fully met.
- --approximation arg          approximation (linear, spline, or exact) to use
- --factor arg                 approximation factor: higher results in a finer-grained approximation
- --force_cap arg              max allowed force; lower values more gently minimize clashing structures
- --user_grid arg              Autodock map file for user grid data based calculations
- --user_grid_lambda arg       Scales user_grid and functional scoring
- --print_terms                Print all available terms with default parameterizations
- --print_atom_types           Print all available atom types  
-
- **Output**
-
- --out arg      output file name, format taken from file extension
- --out_flex arg        output file for flexible receptor residues
- --atom_terms arg      optionally write per-atom interaction term values
- --atom_term_data      embedded per-atom 
-                       interaction terms in output sd data
-
- **Misc**
-
- --seed arg                  explicit random seed
- --exhaustiveness arg        exhaustiveness of the global search (roughly proportional to time)
- --num_modes arg             maximum number of binding modes to generate
- --energy_range arg          maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)
- --min_rmsd_filter arg      rmsd value used to filter final poses to remove redundancy
- --addH arg                 automatically add hydrogens 
-                            in ligands (on by default)
+    **Scoring and minimization options:**
+      --scoring arg                specify alternative builtin scoring function
+      --custom_scoring arg         custom scoring function file
+      --custom_atoms arg           custom atom type parameters file
+      --score_only                 score provided ligand pose
+      --local_only                 local search only using autobox (you probably 
+                                   want to use --minimize)
+      --minimize                   energy minimization
+      --randomize_only             generate random poses, attempting to avoid 
+                                   clashes
+      --minimize_iters arg         number iterations of steepest descent; default 
+                                   scales with rotors and usually isn't sufficient 
+                                   for convergence
+      --accurate_line              use accurate line search
+      --minimize_early_term        stop minimization before convergence conditions 
+                                   are fully met
+      --approximation arg          approximation (linear, spline, or exact) to use
+      --factor arg                 approximation factor: higher results in a 
+                                   finer-grained approximation
+      --force_cap arg              max allowed force; lower values more gently 
+                                   minimize clashing structures
+      --user_grid arg              Autodock map file for user grid data based 
+                                   calculations
+      --user_grid_lambda arg       scales user_grid and functional scoring
+      --print_terms                print all available terms with default 
+                                   parameterizations
+      --print_atom_types           print all available atom types
+    
+    **Misc (optional):**
+      --cpu arg                  the number of CPUs to use (the default is to try 
+                                 to detect the number of CPUs or, failing that, use
+                                 1)
+      --seed arg                 explicit random seed
+      --exhaustiveness arg       exhaustiveness of the global search (roughly 
+                                 proportional to time)
+      --num_modes arg            maximum number of binding modes to generate
+      --energy_range arg         maximum energy difference between the best binding
+                                 mode and the worst one displayed (kcal/mol)
+      --min_rmsd_filter arg      rmsd value used to filter final poses to remove 
+                                 redundancy
+      --addH arg                 automatically add hydrogens in ligands (on by 
+                                 default)
 
         ]]>
     </help>