Mercurial > repos > marpiech > norwich_tools_dock
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 |
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--- 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
