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comparison galaxy_stubs/ConstraintsFinder.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: [Docking]-->
4 <tool id="ConstraintsFinder" name="ConstraintsFinder" version="1.1.0">
5 <description>find strongly interacting residues</description>
6 <macros>
7 <token name="@EXECUTABLE@">ConstraintsFinder</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>ConstraintsFinder
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_o:
24 -o $param_o
25 #end if
26 #if $adv_opts.adv_opts_selector=='advanced':
27 #if $adv_opts.param_ScoringFunction_filename:
28 -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename
29 #end if
30 #if $adv_opts.param_ScoringFunction_electrostatic_cuton:
31 -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton
32 #end if
33 #if $adv_opts.param_ScoringFunction_electrostatic_cutoff:
34 -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff
35 #end if
36 #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap:
37 -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap
38 #end if
39 #if $adv_opts.param_ScoringFunction_ignore_H_clashes:
40 -ScoringFunction:ignore_H_clashes
41 #end if
42 #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap:
43 -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap
44 #end if
45 #if $adv_opts.param_ScoringFunction_burial_depth_scale:
46 -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale
47 #end if
48 #if $adv_opts.param_ScoringFunction_vdw_cutoff:
49 -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff
50 #end if
51 #if $adv_opts.param_ScoringFunction_nonbonded_cutoff:
52 -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff
53 #end if
54 #if $adv_opts.param_ScoringFunction_hashgrid_size:
55 -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size
56 #end if
57 #if $adv_opts.param_ScoringFunction_vdw_cuton:
58 -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton
59 #end if
60 #if $adv_opts.param_ScoringFunction_hashgrid_resolution:
61 -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution
62 #end if
63 #end if
64 </command>
65 <inputs>
66 <param name="param_rec" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="receptor pdb-file" help="(-rec) "/>
67 <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) "/>
68 <param name="param_option" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="configuration file" help="(-option) "/>
69 <expand macro="advanced_options">
70 <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) "/>
71 <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/>
72 <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/>
73 <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) "/>
74 <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) "/>
75 <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) "/>
76 <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) "/>
77 <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/>
78 <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/>
79 <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/>
80 <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/>
81 <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/>
82 </expand>
83 </inputs>
84 <outputs>
85 <data name="param_o" format="ini"/>
86 </outputs>
87 <help>This tool searches protein residues with which the reference ligand interacts strongly.
88 Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
89
90 As input we need:
91 * a file containing a protonated protein in pdb-format
92 * a file containing a reference ligand.
93 This reference ligand should be located in the binding pocket.
94 Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
95
96 Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.
97
98 </help>
99 </tool>