Mercurial > repos > luis > ball
comparison galaxy_stubs/TaGRes.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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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
3 <!--Proposed Tool Section: [Rescoring]--> | |
4 <tool id="TaGRes" name="TaGRes" version="1.1.0"> | |
5 <description>Target-specific Grid-Rescoring</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">TaGRes</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="stdio"/> | |
11 <expand macro="requirements"/> | |
12 <command>TaGRes | |
13 | |
14 #if $param_rec: | |
15 -rec $param_rec | |
16 #end if | |
17 #if $param_rl: | |
18 -rl $param_rl | |
19 #end if | |
20 #if $param_option: | |
21 -option $param_option | |
22 #end if | |
23 #if $param_i: | |
24 -i $param_i | |
25 #end if | |
26 #if $param_mod: | |
27 -mod $param_mod | |
28 #end if | |
29 #if $param_tf: | |
30 -tf $param_tf | |
31 #end if | |
32 #if $param_o: | |
33 -o $param_o | |
34 #end if | |
35 #if $param_method: | |
36 -method | |
37 #if " " in str($param_method): | |
38 "$param_method" | |
39 #else | |
40 $param_method | |
41 #end if | |
42 #end if | |
43 #if $param_function: | |
44 -function | |
45 #if " " in str($param_function): | |
46 "$param_function" | |
47 #else | |
48 $param_function | |
49 #end if | |
50 #end if | |
51 #if $param_rm: | |
52 -rm $param_rm | |
53 #end if | |
54 #if $adv_opts.adv_opts_selector=='advanced': | |
55 #if $adv_opts.param_ScoringFunction_filename: | |
56 -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename | |
57 #end if | |
58 #if $adv_opts.param_ScoringFunction_electrostatic_cuton: | |
59 -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton | |
60 #end if | |
61 #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: | |
62 -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff | |
63 #end if | |
64 #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: | |
65 -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap | |
66 #end if | |
67 #if $adv_opts.param_ScoringFunction_ignore_H_clashes: | |
68 -ScoringFunction:ignore_H_clashes | |
69 #end if | |
70 #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: | |
71 -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap | |
72 #end if | |
73 #if $adv_opts.param_ScoringFunction_burial_depth_scale: | |
74 -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale | |
75 #end if | |
76 #if $adv_opts.param_ScoringFunction_vdw_cutoff: | |
77 -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff | |
78 #end if | |
79 #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: | |
80 -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff | |
81 #end if | |
82 #if $adv_opts.param_ScoringFunction_hashgrid_size: | |
83 -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size | |
84 #end if | |
85 #if $adv_opts.param_ScoringFunction_vdw_cuton: | |
86 -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton | |
87 #end if | |
88 #if $adv_opts.param_ScoringFunction_hashgrid_resolution: | |
89 -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution | |
90 #end if | |
91 #end if | |
92 </command> | |
93 <inputs> | |
94 <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> | |
95 <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) "/> | |
96 <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> | |
97 <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="compounds to be rescored" help="(-i) "/> | |
98 <param name="param_mod" type="data" format="mod" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="model-file generated by TaGRes-train" help="(-mod) "/> | |
99 <param name="param_tf" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="top-scored fraction of compounds not to be rescored" help="(-tf) "/> | |
100 <param name="param_method" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" help="(-method) "> | |
101 <option value="Rescoring3D">Rescoring3D</option> | |
102 <option value=" Rescoring4D"> Rescoring4D</option> | |
103 <option value=" Rescoring1D"> Rescoring1D</option> | |
104 </param> | |
105 <param name="param_function" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="scoring function: 'MM' or 'PLP'" help="(-function) "> | |
106 <option value="MM">MM</option> | |
107 <option value=" PLP"> PLP</option> | |
108 </param> | |
109 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> | |
110 <expand macro="advanced_options"> | |
111 <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) "/> | |
112 <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> | |
113 <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> | |
114 <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) "/> | |
115 <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) "/> | |
116 <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) "/> | |
117 <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) "/> | |
118 <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> | |
119 <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> | |
120 <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> | |
121 <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> | |
122 <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> | |
123 </expand> | |
124 </inputs> | |
125 <outputs> | |
126 <data name="param_o" format="mol2"/> | |
127 </outputs> | |
128 <help>This tool rescores docking output poses using Target-specific Grid-Rescoring. | |
129 Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool. | |
130 As input TaGRes needs: | |
131 | |
132 * a file containing a protonated protein in pdb-format | |
133 * 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). | |
134 * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein. | |
135 * a regression model file as generated by TaGRes-train for same protein target than the one specified here. | |
136 | |
137 TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy. | |
138 | |
139 Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'. | |
140 | |
141 </help> | |
142 </tool> |