|
2
|
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="SimpleRescorer" name="SimpleRescorer" version="1.1.0">
|
|
|
5 <description>rescore docking results</description>
|
|
|
6 <macros>
|
|
|
7 <token name="@EXECUTABLE@">SimpleRescorer</token>
|
|
|
8 <import>macros.xml</import>
|
|
|
9 </macros>
|
|
|
10 <expand macro="stdio"/>
|
|
|
11 <expand macro="requirements"/>
|
|
|
12 <command>SimpleRescorer
|
|
|
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_o:
|
|
|
27 -o $param_o
|
|
|
28 #end if
|
|
|
29 #if $param_function:
|
|
|
30 -function
|
|
|
31 #if " " in str($param_function):
|
|
|
32 "$param_function"
|
|
|
33 #else
|
|
|
34 $param_function
|
|
|
35 #end if
|
|
|
36 #end if
|
|
|
37 #if $param_rm:
|
|
|
38 -rm $param_rm
|
|
|
39 #end if
|
|
|
40 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
41 #if $adv_opts.param_ScoringFunction_filename:
|
|
|
42 -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename
|
|
|
43 #end if
|
|
|
44 #if $adv_opts.param_ScoringFunction_electrostatic_cuton:
|
|
|
45 -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton
|
|
|
46 #end if
|
|
|
47 #if $adv_opts.param_ScoringFunction_electrostatic_cutoff:
|
|
|
48 -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff
|
|
|
49 #end if
|
|
|
50 #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap:
|
|
|
51 -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap
|
|
|
52 #end if
|
|
|
53 #if $adv_opts.param_ScoringFunction_ignore_H_clashes:
|
|
|
54 -ScoringFunction:ignore_H_clashes
|
|
|
55 #end if
|
|
|
56 #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap:
|
|
|
57 -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap
|
|
|
58 #end if
|
|
|
59 #if $adv_opts.param_ScoringFunction_burial_depth_scale:
|
|
|
60 -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale
|
|
|
61 #end if
|
|
|
62 #if $adv_opts.param_ScoringFunction_vdw_cutoff:
|
|
|
63 -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff
|
|
|
64 #end if
|
|
|
65 #if $adv_opts.param_ScoringFunction_nonbonded_cutoff:
|
|
|
66 -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff
|
|
|
67 #end if
|
|
|
68 #if $adv_opts.param_ScoringFunction_hashgrid_size:
|
|
|
69 -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size
|
|
|
70 #end if
|
|
|
71 #if $adv_opts.param_ScoringFunction_vdw_cuton:
|
|
|
72 -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton
|
|
|
73 #end if
|
|
|
74 #if $adv_opts.param_ScoringFunction_hashgrid_resolution:
|
|
|
75 -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution
|
|
|
76 #end if
|
|
|
77 #end if
|
|
|
78 </command>
|
|
|
79 <inputs>
|
|
|
80 <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/>
|
|
|
81 <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) "/>
|
|
|
82 <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/>
|
|
|
83 <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) "/>
|
|
|
84 <param name="param_function" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="scoring function: 'MM', 'PLP' or 'PB'" help="(-function) ">
|
|
|
85 <option value="MM">MM</option>
|
|
|
86 <option value=" PLP"> PLP</option>
|
|
|
87 <option value=" PB"> PB</option>
|
|
|
88 </param>
|
|
|
89 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
|
|
|
90 <expand macro="advanced_options">
|
|
|
91 <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) "/>
|
|
|
92 <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/>
|
|
|
93 <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/>
|
|
|
94 <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) "/>
|
|
|
95 <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) "/>
|
|
|
96 <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) "/>
|
|
|
97 <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) "/>
|
|
|
98 <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/>
|
|
|
99 <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/>
|
|
|
100 <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/>
|
|
|
101 <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/>
|
|
|
102 <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/>
|
|
|
103 </expand>
|
|
|
104 </inputs>
|
|
|
105 <outputs>
|
|
|
106 <data name="param_o" format="mol2"/>
|
|
|
107 </outputs>
|
|
|
108 <help>This tool rescores docking output poses.
|
|
|
109 A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).
|
|
|
110
|
|
|
111 As input we need:
|
|
|
112 * a file containing a protonated protein in pdb-format
|
|
|
113 * 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).
|
|
|
114 * 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.
|
|
|
115
|
|
|
116 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'.
|
|
|
117
|
|
|
118 </help>
|
|
|
119 </tool>
|
