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comparison smina.xml @ 2:0faa03a92843 draft default tip

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author dzesikah
date Fri, 26 Aug 2016 10:19:49 -0400
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1:ad4bc82457e5 2:0faa03a92843
1 <tool id="smina" name="smina" version="0.1.0">
2 <requirements>
3 </requirements>
4 <stdio>
5 <exit_code range="1:" />
6 </stdio>
7 <command>
8 <![CDATA[
9 cat $receptor > receptor.pdbqt;
10 cat $ligand > ligand.pdbqt;
11 $__tool_directory__/tools/smina/smina.static
12 --receptor receptor.pdbqt
13 --ligand ligand.pdbqt
14
15 #if $flex
16 --flex $flex
17 #end if
18 #if $flexres
19 --flexres $flexres
20 #end if
21 #if $flexdist_ligand
22 --flexdist_ligand $flexdist_ligand
23 #end if
24 #if $flexdist
25 --flexdist $flexdist
26 #end if
27
28 --center_x $center_x
29 --center_y $center_y
30 --center_z $center_z
31 --size_x $size_x
32 --size_y $size_y
33 --size_z $size_z
34
35 #if $autobox_ligand
36 --autobox_ligand $autobox_ligand
37 #end if
38 #if $autobox_add
39 --autobox_add $autobox_add
40 #end if
41 #if $no_lig=="true"
42 --no_lig
43 #end if
44
45 --scoring $scoring
46 #if $custom_scoring
47 --custom_scoring $custom_scoring
48 #end if
49 #if $custom_atoms
50 --custom_atoms $custom_atoms
51 #end if
52 #if $score_only=="true"
53 --score_only
54 #end if
55 #if $local_only=="true"
56 --local_only
57 #end if
58 #if $minimize=="true"
59 --minimize
60 #end if
61 #if $randomize_only=="true"
62 --randomize_only
63 #end if
64 #if $minimize_iters
65 --minimize_iters $minimize_iters
66 #end if
67
68 --seed 1000 > $output;
69 cat $output > /tmp/ouput
70 ]]>
71 </command>
72 <inputs>
73 <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" />
74 <param name="ligand" type="data" format="data" label="ligand: ligand(s)" />
75
76 <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" />
77 <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" />
78 <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" />
79 <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" />
80
81 <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" />
82 <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" />
83 <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" />
84 <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" />
85 <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" />
86 <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" />
87
88 <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" />
89 <param name="autobox_add" type="float" value="4" label="autobox_add: Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" />
90 <param name="no_lig" type="select" label="no_lig: no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" optional="true">
91 <option value="false" selected="true">Don't use this option</option>
92 <option value="true">Use this option</option>
93 </param>
94
95 <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true">
96 <option value="default" selected="true">default</option>
97 <option value="ad4_scoring">ad4_scoring</option>
98 <option value="dkoes_fast">dkoes_fast</option>
99 <option value="dkoes_scoring">dkoes_scoring</option>
100 <option value="dkoes_scoring_old">dkoes_scoring_old</option>
101 <option value="vina">vina</option>
102 <option value="vinardo">vinardo</option>
103 </param>
104 <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" />
105 <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" />
106 <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true">
107 <option value="false" selected="true">Don't use this option</option>
108 <option value="true">Use this option</option>
109 </param>
110 <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true">
111 <option value="false" selected="true">Don't use this option</option>
112 <option value="true">Use this option</option>
113 </param>
114 <param name="minimize" type="select" label="minimize: energy minimization" optional="true">
115 <option value="false" selected="true">Don't use this option</option>
116 <option value="true">Use this option</option>
117 </param>
118 <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true">
119 <option value="false" selected="true">Don't use this option</option>
120 <option value="true">Use this option</option>
121 </param>
122 <param name="minimize_iters" type="integer" label="minimize_iters: number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" />
123 </inputs>
124 <outputs>
125 <data name="output" format="data" />
126 </outputs>
127 <tests>
128 <test>
129 <param name="receptor" value="smina/protein.pdbqt" />
130 <param name="ligand" value="smina/ligand.pdbqt" />
131 <param name="center_x" value="11" />
132 <param name="center_y" value="90.5" />
133 <param name="center_z" value="57.5" />
134 <param name="size_x" value="22" />
135 <param name="size_y" value="24" />
136 <param name="size_z" value="28" />
137 <output name="output" file="smina/output_smina" />
138 </test>
139 </tests>
140 <help>
141 "Smina help"
142 </help>
143 <citations>
144 <citation type="bibtex">
145 @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, }
146 </citation>
147 </citations>
148 </tool>