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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty
author earlhaminst
date Tue, 08 May 2018 19:08:15 -0400
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-1:000000000000 0:7c0bb0c48a27
1 <tool id="smina" name="smina" version="1.0">
2 <description>Scoring and Minimization with AutoDock Vina</description>
3 <requirements>
4 <requirement type="package" version="2017.11.9">smina</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 ln -s '$input.receptor' receptor.pdbqt &&
8 ln -s '$input.ligand' ligand.pdbqt &&
9 smina
10 --receptor receptor.pdbqt
11 --ligand ligand.pdbqt
12 #if $input.flex
13 --flex '$input.flex'
14 #end if
15 #if $input.flexres
16 --flexres '$input.flexres'
17 #end if
18 #if $input.flexdist_ligand
19 --flexdist_ligand '$input.flexdist_ligand'
20 #end if
21 #if str($input.flexdist)
22 --flexdist $input.flexdist
23 #end if
24
25 --center_x $search_space.center_x
26 --center_y $search_space.center_y
27 --center_z $search_space.center_z
28 --size_x $search_space.size_x
29 --size_y $search_space.size_y
30 --size_z $search_space.size_z
31 #if $search_space.autobox_ligand
32 --autobox_ligand '$search_space.autobox_ligand'
33 #end if
34 #if str($search_space.autobox_add)
35 --autobox_add $search_space.autobox_add
36 #end if
37 $search_space.no_lig
38
39 --out ligand_out.pdbqt
40 #if $output_sect.out_flex
41 --out_flex '$out_flex_output'
42 #end if
43 #if $output_sect.log
44 --log '$output_log'
45 #end if
46 #if $output_sect.atom_terms
47 --atom_terms '$atom_terms_output'
48 #end if
49 $output_sect.atom_term_data
50
51 --scoring $scoring_and_minimization.scoring
52 #if $scoring_and_minimization.custom_scoring
53 --custom_scoring '$scoring_and_minimization.custom_scoring'
54 #end if
55 #if $scoring_and_minimization.custom_atoms
56 --custom_atoms '$scoring_and_minimization.custom_atoms'
57 #end if
58 $scoring_and_minimization.score_only
59 $scoring_and_minimization.local_only
60 $scoring_and_minimization.minimize
61 $scoring_and_minimization.randomize_only
62 --minimize_iters $scoring_and_minimization.minimize_iters
63 $scoring_and_minimization.accurate_line
64 $scoring_and_minimization.minimize_early_term
65 #if $scoring_and_minimization.approximation
66 --approximation $scoring_and_minimization.approximation
67 #end if
68 #if $scoring_and_minimization.factor
69 --factor $scoring_and_minimization.factor
70 #end if
71 #if str($scoring_and_minimization.force_cap)
72 --force_cap $scoring_and_minimization.force_cap
73 #end if
74 #if str($scoring_and_minimization.user_grid)
75 --user_grid $scoring_and_minimization.user_grid
76 #end if
77 --user_grid_lambda $scoring_and_minimization.user_grid_lambda
78 $scoring_and_minimization.print_terms
79 $scoring_and_minimization.print_atom_types
80
81 --cpu \${GALAXY_SLOTS:-1}
82 #if str($misc.seed)
83 --seed $misc.seed
84 #end if
85 --exhaustiveness $misc.exhaustiveness
86 --num_modes $misc.num_modes
87 --energy_range $misc.energy_range
88 --min_rmsd_filter $misc.min_rmsd_filter
89 $misc.addH
90 ]]></command>
91 <inputs>
92 <section name="input" title="Input" expanded="True">
93 <param argument="--receptor" type="data" format="pdbqt" label="Rigid part of the receptore" />
94 <param argument="--ligand" type="data" format="pdbqt" label="Ligand(s)" />
95 <param argument="--flex" type="data" format="pdbqt" optional="true" label="Flexible side chains, if any" />
96 <param argument="--flexres" type="text" optional="true" label="Flexible side chains specified by comma separated list of chain:resid" />
97 <param argument="--flexdist_ligand" type="data" format="data" optional="true" label="Ligand to use for flexdist" />
98 <param argument="--flexdist" type="float" optional="true" label="Set all side chains within specified distance to flexdist_ligand to flexible" />
99 </section>
100 <section name="search_space" title="Search space" expanded="True">
101 <param argument="--center_x" type="float" value="0" label="X coordinate of the center" />
102 <param argument="--center_y" type="float" value="0" label="Y coordinate of the center" />
103 <param argument="--center_z" type="float" value="0" label="Z coordinate of the center" />
104 <param argument="--size_x" type="integer" value="1" label="Size in the X dimension" />
105 <param argument="--size_y" type="integer" value="1" label="Size in the Y dimension" />
106 <param argument="--size_z" type="integer" value="1" label="Size in the Z dimension" />
107
108 <param argument="--autobox_ligand" type="data" format="data" optional="true" label="Ligand to use for autobox" />
109 <param argument="--autobox_add" type="float" optional="true" label="Amount of buffer space to add to auto-generated box text" />
110 <param argument="--no_lig" type="boolean" truevalue="--no_lig" falsevalue="" label="No ligand; for sampling/minimizing flexible residues" />
111 </section>
112 <section name="output_sect" title="Output">
113 <param argument="--out_flex" type="boolean" label="Write flexible receptor residues" />
114 <param argument="--log" type="boolean" label="Write log file" />
115 <param argument="--atom_terms" type="boolean" label="Write per-atom interaction term values" />
116 <param argument="--atom_term_data" type="boolean" truevalue="--atom_term_data" falsevalue="" label="Embedded per-atom interaction terms in output sd data" />
117 </section>
118 <section name="scoring_and_minimization" title="Scoring and minimization options">
119 <param argument="--scoring" type="select" label="Specify alternative builtin scoring function">
120 <option value="default" selected="true">default</option>
121 <option value="ad4_scoring">ad4_scoring</option>
122 <option value="dkoes_fast">dkoes_fast</option>
123 <option value="dkoes_scoring">dkoes_scoring</option>
124 <option value="dkoes_scoring_old">dkoes_scoring_old</option>
125 <option value="vina">vina</option>
126 <option value="vinardo">vinardo</option>
127 </param>
128 <param argument="--custom_scoring" type="data" format="data" optional="true" label="Custom scoring function file" />
129 <param argument="--custom_atoms" type="data" format="data" optional="true" label="Custom atom type parameters file" />
130 <param argument="--score_only" type="boolean" truevalue="--score_only" falsevalue="" label="Score provided ligand pose" />
131 <param argument="--local_only" type="boolean" truevalue="--local_only" falsevalue="" label="Local search only using autobox" />
132 <param argument="--minimize" type="boolean" truevalue="--minimize" falsevalue="" label="Energy minimization" />
133 <param argument="--randomize_only" type="boolean" truevalue="--randomize_only" falsevalue="" label="Generate random poses, attempting to avoid clashes" />
134 <param argument="--minimize_iters" type="integer" value="0" label="Number iterations of steepest descent" />
135 <param argument="--accurate_line" type="boolean" truevalue="--accurate_line" falsevalue="" label="Accurate line search" />
136 <param argument="--minimize_early_term" type="boolean" truevalue="--minimize_early_term" falsevalue="" label="Stop minimization before convergence conditions are fully met" />
137 <param argument="--approximation" type="select" optional="true" label="Approximation">
138 <option value="linear">linear</option>
139 <option value="spline">spline</option>
140 <option value="exact">exact</option>
141 </param>
142 <param argument="--factor" type="float" min="0" optional="true" label="Approximation factor: higher results in a finer-grained approximation" />
143 <param argument="--force_cap" type="float" optional="true" label="Max allowed force; lower values more gently minimize clashing structures" />
144 <param argument="--user_grid" type="float" optional="true" label="Autodock map file for user grid data based calculations" />
145 <param argument="--user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring" />
146 <param argument="--print_terms" type="boolean" truevalue="--print_terms" falsevalue="" label="Print all available terms with default parameterizations" />
147 <param argument="--print_atom_types" type="boolean" truevalue="--print_atom_types" falsevalue="" label="Print all available atom types" />
148 </section>
149 <section name="misc" title="Misc">
150 <param argument="--seed" type="integer" optional="true" label="Explicit random seed" />
151 <param argument="--exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" />
152 <param argument="--num_modes" type="integer" min="1" value="9" label="Maximum number of binding modes to generate" />
153 <param argument="--energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" />
154 <param argument="--min_rmsd_filter" type="float" value="1" label="Rmsd value used to filter final poses to remove redundancy" />
155 <param argument="--addH" type="boolean" truevalue="" falsevalue="--addH false" checked="true" label="Automatically add hydrogens in ligands" />
156 </section>
157 </inputs>
158 <outputs>
159 <data name="output" format="pdbqt" from_work_dir="ligand_out.pdbqt" />
160 <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">
161 <filter>output_sect['out_flex']</filter>
162 </data>
163 <data name="output_log" format="txt" label="smina: log file">
164 <filter>output_sect['log']</filter>
165 </data>
166 <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">
167 <filter>output_sect['atom_terms']</filter>
168 </data>
169 </outputs>
170 <tests>
171 <test>
172 <param name="receptor" value="protein.pdbqt" />
173 <param name="ligand" value="ligand.pdbqt" />
174 <param name="center_x" value="11" />
175 <param name="center_y" value="90.5" />
176 <param name="center_z" value="57.5" />
177 <param name="size_x" value="22" />
178 <param name="size_y" value="24" />
179 <param name="size_z" value="28" />
180 <param name="log" value="True" />
181 <param name="seed" value="1000" />
182 <param name="num_modes" value="5" />
183 <output name="output" file="ligand_out.pdbqt" />
184 <output name="output_log" file="output_smina" />
185 </test>
186 </tests>
187 <help><![CDATA[
188 ************
189 Description
190 ************
191
192 `smina <https://sourceforge.net/projects/smina/>`_ is a fork of `AutoDock Vina <http://vina.scripps.edu/>`_ that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
193 ]]></help>
194 <citations>
195 <citation type="doi">10.1021/ci300604z</citation>
196 </citations>
197 </tool>