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comparison galaxy_stubs/SimpleRescorer.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1:31013b5cd066 2:605370bc1def
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="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="reference-ligand" help="(-rl) "/>
82 <param name="param_option" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="compounds to be rescored" help="(-i) "/>
84 <param name="param_function" type="select" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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>