diff psovina.xml @ 3:8c2e85bb2ce9 draft

planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
author marpiech
date Tue, 20 Sep 2016 09:57:24 -0400
parents 958fa7ba4715
children
line wrap: on
line diff
--- a/psovina.xml	Wed Sep 14 09:47:48 2016 -0400
+++ b/psovina.xml	Tue Sep 20 09:57:24 2016 -0400
@@ -65,17 +65,17 @@
     </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="pdbqt" label="ligand(s)" help="(--ligand)"/>
-            <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex)"/>
+            <param name="receptor" type="data" format="pdbqt" label="Rigid part of the receptore" help="(--receptor)"/>
+            <param name="ligand" type="data" format="pdbqt" label="Ligand(s)" help="(--ligand)"/>
+            <param name="flex" type="data" format="pdbqt" label="Flexible side chains, if any" optional="true" help="(--flex)"/>
         </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)"/>
         </section>
         <section name="pso_parameters" title="PSO parameters" >
             <param name="num_particles" type="integer" value="8" label="Number of particles of each thread" help="(--num_particles)"/>
@@ -90,33 +90,33 @@
             </param>
         </section>
         <section name="advanced_options" title="Advanced option">
-            <param name="score_only" type="select" label="score only - search space can be omitted" help="(--score_only)">
+            <param name="score_only" type="select" label="Score only - search space can be omitted" 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="do local search only" help="(--local_only)">
+            <param name="local_only" type="select" label="Do local search only" help="(--local_only)">
                 <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="randomize input, attempting to avoid clashes" help="(--randomize_only)">
+            <param name="randomize_only" type="select" label="Randomize input, 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="weight_gauss1" type="float" value="-0.035579" label="gauss_1 weight" help="(--weight_gauss1)"/>
             <param name="weight_gauss2" type="float" value="-0.005156" label="gauss_2 weight" help="(--weight_gauss2)"/>
-            <param name="weight_repulsion" type="float" value="0.84024500000000002" label="repulsion weight" help="(--weight_repulsion)"/>
-            <param name="weight_hydrophobic" type="float" value="-0.035069000000000003" label="hydrophobic weight" help="(--weight_hydrophobic)"/>
+            <param name="weight_repulsion" type="float" value="0.84024500000000002" label="Repulsion weight" help="(--weight_repulsion)"/>
+            <param name="weight_hydrophobic" type="float" value="-0.035069000000000003" label="Hydrophobic weight" help="(--weight_hydrophobic)"/>
             <param name="weight_hydrogen" type="float" value="-0.58743900000000004" label="Hydrogen bond weight" help="(--weight_hydrogen)"/>
             <param name="weight_rot" type="float" value="0.058459999999999998" label="N_rot weight" help="(--weight_rot)"/>
         </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="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)"/>
         </section>
     </inputs>
     <outputs>
@@ -180,10 +180,10 @@
       --size_z arg          size in the Z dimension (Angstroms)
     
     **PSO parameters (optional):**
-      --num_particles arg      Number of particles of each thread
-      --w arg                  Inertia weight
-      --c1 arg                 Cognitive weight
-      --c2 arg                 Social weight
+      --num_particles arg      number of particles of each thread
+      --w arg                  inertia weight
+      --c1 arg                 cognitive weight
+      --c2 arg                 social weight
     
     **Output (optional):**
       --log           optionally, write log file