Mercurial > repos > luis > ball
diff galaxy_stubs/TaGRes-train.xml @ 2:605370bc1def draft default tip
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| author | luis |
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| date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/TaGRes-train.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,139 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Rescoring]--> +<tool id="TaGResTrain" name="TaGResTrain" version="1.1.0"> + <description>Target-specific Grid-Rescoring, training</description> + <macros> + <token name="@EXECUTABLE@">TaGResTrain</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>TaGResTrain + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_option: + -option $param_option +#end if +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_method: + -method + #if " " in str($param_method): + "$param_method" + #else + $param_method + #end if +#end if +#if $param_function: + -function + #if " " in str($param_function): + "$param_function" + #else + $param_function + #end if +#end if +#if $param_exp: + -exp "$param_exp" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="training compound data set" help="(-i) "/> + <param name="param_method" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" help="(-method) "> + <option value="Rescoring3D">Rescoring3D</option> + <option value=" Rescoring4D"> Rescoring4D</option> + <option value=" Rescoring1D"> Rescoring1D</option> + </param> + <param name="param_function" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="scoring function: 'MM' or 'PLP'" help="(-function) "> + <option value="MM">MM</option> + <option value=" PLP"> PLP</option> + </param> + <param name="param_exp" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="property-tag name containing experimentally determined binding-free-energies" help="(-exp) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mod"/> + </outputs> + <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes). +As input we need: + + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein. + +A scoring function is applied and an interaction-grid is thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it. + +The output of TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written. + +</help> +</tool>