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comparison galaxy_stubs/CrystalGenerator.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: [Structure Creation]-->
4 <tool id="CrystalGenerator" name="CrystalGenerator" version="VERSION">
5 <description>creates crystals</description>
6 <macros>
7 <token name="@EXECUTABLE@">CrystalGenerator</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>CrystalGenerator
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_o:
18 -o $param_o
19 #end if
20 #if $param_sg:
21 -sg
22 #if " " in str($param_sg):
23 "$param_sg"
24 #else
25 $param_sg
26 #end if
27 #end if
28 #if $param_axis_a:
29 -axis_a $param_axis_a
30 #end if
31 #if $param_axis_b:
32 -axis_b $param_axis_b
33 #end if
34 #if $param_axis_c:
35 -axis_c $param_axis_c
36 #end if
37 #if $param_angle_alpha:
38 -angle_alpha $param_angle_alpha
39 #end if
40 #if $param_angle_beta:
41 -angle_beta $param_angle_beta
42 #end if
43 #if $param_angle_gamma:
44 -angle_gamma $param_angle_gamma
45 #end if
46 #if $param_from_uc_a:
47 -from_uc_a $param_from_uc_a
48 #end if
49 #if $param_from_uc_b:
50 -from_uc_b $param_from_uc_b
51 #end if
52 #if $param_from_uc_c:
53 -from_uc_c $param_from_uc_c
54 #end if
55 #if $param_to_uc_a:
56 -to_uc_a $param_to_uc_a
57 #end if
58 #if $param_to_uc_b:
59 -to_uc_b $param_to_uc_b
60 #end if
61 #if $param_to_uc_c:
62 -to_uc_c $param_to_uc_c
63 #end if
64 </command>
65 <inputs>
66 <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-i) "/>
67 <param name="param_sg" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="space group symbol in Herman-Mauguin notation" help="(-sg) ">
68 <option value="P 1">P 1</option>
69 <option value=" P 1-"> P 1-</option>
70 <option value=" P 2"> P 2</option>
71 <option value=" P 21"> P 21</option>
72 <option value=" C 2"> C 2</option>
73 <option value=" P M"> P M</option>
74 <option value=" P C"> P C</option>
75 <option value=" C M"> C M</option>
76 <option value=" C C"> C C</option>
77 <option value=" P 2/M"> P 2/M</option>
78 <option value=" P 21/M"> P 21/M</option>
79 <option value=" C 2/M"> C 2/M</option>
80 <option value=" P 2/C"> P 2/C</option>
81 <option value=" P 21/C"> P 21/C</option>
82 <option value=" C 2/C"> C 2/C</option>
83 <option value=" P 2 2 2"> P 2 2 2</option>
84 <option value=" P 2 2 21"> P 2 2 21</option>
85 <option value=" P 21 21 2"> P 21 21 2</option>
86 <option value=" P 21 21 21"> P 21 21 21</option>
87 <option value=" C 2 2 21"> C 2 2 21</option>
88 <option value=" C 2 2 2"> C 2 2 2</option>
89 <option value=" F 2 2 2"> F 2 2 2</option>
90 <option value=" I 2 2 2"> I 2 2 2</option>
91 <option value=" I 21 21 21"> I 21 21 21</option>
92 <option value=" P M M 2"> P M M 2</option>
93 <option value=" P M C 21"> P M C 21</option>
94 <option value=" P C C 2"> P C C 2</option>
95 <option value=" P M A 2"> P M A 2</option>
96 <option value=" P C A 21"> P C A 21</option>
97 <option value=" P N C 2"> P N C 2</option>
98 <option value=" P M N 21"> P M N 21</option>
99 <option value=" P B A 2"> P B A 2</option>
100 <option value=" P N A 21"> P N A 21</option>
101 <option value=" P N N 2"> P N N 2</option>
102 <option value=" C M M 2"> C M M 2</option>
103 <option value=" C M C 21"> C M C 21</option>
104 <option value=" C C C 2"> C C C 2</option>
105 <option value=" A M M 2"> A M M 2</option>
106 <option value=" A B M 2"> A B M 2</option>
107 <option value=" A M A 2"> A M A 2</option>
108 <option value=" A B A 2"> A B A 2</option>
109 <option value=" F M M 2"> F M M 2</option>
110 <option value=" F D D 2"> F D D 2</option>
111 <option value=" I M M 2"> I M M 2</option>
112 <option value=" I B A 2"> I B A 2</option>
113 <option value=" I M A 2"> I M A 2</option>
114 <option value=" P M M M"> P M M M</option>
115 <option value=" P N N N"> P N N N</option>
116 <option value=" P C C M"> P C C M</option>
117 <option value=" P B A N"> P B A N</option>
118 <option value=" P M M A"> P M M A</option>
119 <option value=" P N N A"> P N N A</option>
120 <option value=" P M N A"> P M N A</option>
121 <option value=" P C C A"> P C C A</option>
122 <option value=" P B A M"> P B A M</option>
123 <option value=" P C C N"> P C C N</option>
124 <option value=" P B C M"> P B C M</option>
125 <option value=" P N N M"> P N N M</option>
126 <option value=" P M M N"> P M M N</option>
127 <option value=" P B C N"> P B C N</option>
128 <option value=" P B C A"> P B C A</option>
129 <option value=" P N M A"> P N M A</option>
130 <option value=" C M C M"> C M C M</option>
131 <option value=" C M C A"> C M C A</option>
132 <option value=" C M M M"> C M M M</option>
133 <option value=" C C C M"> C C C M</option>
134 <option value=" C M M A"> C M M A</option>
135 <option value=" C C C A"> C C C A</option>
136 <option value=" F M M M"> F M M M</option>
137 <option value=" F D D D"> F D D D</option>
138 <option value=" I M M M"> I M M M</option>
139 <option value=" I B A M"> I B A M</option>
140 <option value=" I B C A"> I B C A</option>
141 <option value=" I M M A"> I M M A</option>
142 <option value=" P 4"> P 4</option>
143 <option value=" P 41"> P 41</option>
144 <option value=" P 42"> P 42</option>
145 <option value=" P 43"> P 43</option>
146 <option value=" I 4"> I 4</option>
147 <option value=" I 41"> I 41</option>
148 <option value=" P -4"> P -4</option>
149 <option value=" I -4"> I -4</option>
150 <option value=" P 4/M"> P 4/M</option>
151 <option value=" P 42/M"> P 42/M</option>
152 <option value=" P 4/N"> P 4/N</option>
153 <option value=" P 42/N"> P 42/N</option>
154 <option value=" I 4/M"> I 4/M</option>
155 <option value=" I 41/A"> I 41/A</option>
156 <option value=" P 4 2 2"> P 4 2 2</option>
157 <option value=" P 4 21 2"> P 4 21 2</option>
158 <option value=" P 41 2 2"> P 41 2 2</option>
159 <option value=" P 41 21 2"> P 41 21 2</option>
160 <option value=" P 42 2 2"> P 42 2 2</option>
161 <option value=" P 42 21 2"> P 42 21 2</option>
162 <option value=" P 43 2 2"> P 43 2 2</option>
163 <option value=" P 43 21 2"> P 43 21 2</option>
164 <option value=" I 4 2 2"> I 4 2 2</option>
165 <option value=" I 41 2 2"> I 41 2 2</option>
166 <option value=" P 4 M M"> P 4 M M</option>
167 <option value=" P 4 B M"> P 4 B M</option>
168 <option value=" P 42 C M"> P 42 C M</option>
169 <option value=" P 42 N M"> P 42 N M</option>
170 <option value=" P 4 C C"> P 4 C C</option>
171 <option value=" P 4 N C"> P 4 N C</option>
172 <option value=" P 42 M C"> P 42 M C</option>
173 <option value=" P 42 B C"> P 42 B C</option>
174 <option value=" I 4 M M"> I 4 M M</option>
175 <option value=" I 4 C M"> I 4 C M</option>
176 <option value=" I 41 M D"> I 41 M D</option>
177 <option value=" I 41 C D"> I 41 C D</option>
178 <option value=" P -4 2 M"> P -4 2 M</option>
179 <option value=" P -4 2 C"> P -4 2 C</option>
180 <option value=" P -4 21 M"> P -4 21 M</option>
181 <option value=" P -4 21 C"> P -4 21 C</option>
182 <option value=" P -4 M 2"> P -4 M 2</option>
183 <option value=" P -4 C 2"> P -4 C 2</option>
184 <option value=" P -4 B 2"> P -4 B 2</option>
185 <option value=" P -4 N 2"> P -4 N 2</option>
186 <option value=" I -4 M 2"> I -4 M 2</option>
187 <option value=" I -4 C 2"> I -4 C 2</option>
188 <option value=" I -4 2 M"> I -4 2 M</option>
189 <option value=" I -4 2 D"> I -4 2 D</option>
190 <option value=" P 4/M M M"> P 4/M M M</option>
191 <option value=" P 4/M C C"> P 4/M C C</option>
192 <option value=" P 4/N B M"> P 4/N B M</option>
193 <option value=" P 4/N N C"> P 4/N N C</option>
194 <option value=" P 4/M B M"> P 4/M B M</option>
195 <option value=" P 4/M N C"> P 4/M N C</option>
196 <option value=" P 4/N M M"> P 4/N M M</option>
197 <option value=" P 4/N C C"> P 4/N C C</option>
198 <option value=" P 42/M M C"> P 42/M M C</option>
199 <option value=" P 42/M C M"> P 42/M C M</option>
200 <option value=" P 42/N B C"> P 42/N B C</option>
201 <option value=" P 42/N N M"> P 42/N N M</option>
202 <option value=" P 42/M B C"> P 42/M B C</option>
203 <option value=" P 42/M N M"> P 42/M N M</option>
204 <option value=" P 42/N M C"> P 42/N M C</option>
205 <option value=" P 42/N C M"> P 42/N C M</option>
206 <option value=" I 4/M M M"> I 4/M M M</option>
207 <option value=" I 4/M C M"> I 4/M C M</option>
208 <option value=" I 41/A M D"> I 41/A M D</option>
209 <option value=" I 41/A C D"> I 41/A C D</option>
210 <option value=" P 3"> P 3</option>
211 <option value=" P 31"> P 31</option>
212 <option value=" P 32"> P 32</option>
213 <option value=" R 3"> R 3</option>
214 <option value=" P -3"> P -3</option>
215 <option value=" R -3"> R -3</option>
216 <option value=" P 3 1 2"> P 3 1 2</option>
217 <option value=" P 3 2 1"> P 3 2 1</option>
218 <option value=" P 31 1 2"> P 31 1 2</option>
219 <option value=" P 31 2 1"> P 31 2 1</option>
220 <option value=" P 32 1 2"> P 32 1 2</option>
221 <option value=" P 32 2 1"> P 32 2 1</option>
222 <option value=" R 3 2"> R 3 2</option>
223 <option value=" P 3 M 1"> P 3 M 1</option>
224 <option value=" P 3 1 M"> P 3 1 M</option>
225 <option value=" P 3 C 1"> P 3 C 1</option>
226 <option value=" P 3 1 C"> P 3 1 C</option>
227 <option value=" R 3 M"> R 3 M</option>
228 <option value=" R 3 C"> R 3 C</option>
229 <option value=" P -3 1 M"> P -3 1 M</option>
230 <option value=" P -3 1 C"> P -3 1 C</option>
231 <option value=" P -3 M 1"> P -3 M 1</option>
232 <option value=" P -3 C 1"> P -3 C 1</option>
233 <option value=" R -3 M"> R -3 M</option>
234 <option value=" R -3 C"> R -3 C</option>
235 <option value=" P 6"> P 6</option>
236 <option value=" P 61"> P 61</option>
237 <option value=" P 65"> P 65</option>
238 <option value=" P 62"> P 62</option>
239 <option value=" P 64"> P 64</option>
240 <option value=" P 63"> P 63</option>
241 <option value=" P -6"> P -6</option>
242 <option value=" P 6/M"> P 6/M</option>
243 <option value=" P 63/M"> P 63/M</option>
244 <option value=" P 6 2 2"> P 6 2 2</option>
245 <option value=" P 61 2 2"> P 61 2 2</option>
246 <option value=" P 65 2 2"> P 65 2 2</option>
247 <option value=" P 62 2 2"> P 62 2 2</option>
248 <option value=" P 64 2 2"> P 64 2 2</option>
249 <option value=" P 63 2 2"> P 63 2 2</option>
250 <option value=" P 6 M M"> P 6 M M</option>
251 <option value=" P 6 C C"> P 6 C C</option>
252 <option value=" P 63 C M"> P 63 C M</option>
253 <option value=" P 63 M C"> P 63 M C</option>
254 <option value=" P -6 M 2"> P -6 M 2</option>
255 <option value=" P -6 C 2"> P -6 C 2</option>
256 <option value=" P -6 2 M"> P -6 2 M</option>
257 <option value=" P -6 2 C"> P -6 2 C</option>
258 <option value=" P 6/M M M"> P 6/M M M</option>
259 <option value=" P 6/M C C"> P 6/M C C</option>
260 <option value=" P 63/M C M"> P 63/M C M</option>
261 <option value=" P 63/M M C"> P 63/M M C</option>
262 <option value=" P 2 3"> P 2 3</option>
263 <option value=" F 2 3"> F 2 3</option>
264 <option value=" I 2 3"> I 2 3</option>
265 <option value=" P 21 3"> P 21 3</option>
266 <option value=" I 21 3"> I 21 3</option>
267 <option value=" P M -3"> P M -3</option>
268 <option value=" P N -3"> P N -3</option>
269 <option value=" F M -3"> F M -3</option>
270 <option value=" F D -3"> F D -3</option>
271 <option value=" I M -3"> I M -3</option>
272 <option value=" P A -3"> P A -3</option>
273 <option value=" I A -3"> I A -3</option>
274 <option value=" P 4 3 2"> P 4 3 2</option>
275 <option value=" P 42 3 2"> P 42 3 2</option>
276 <option value=" F 4 3 2"> F 4 3 2</option>
277 <option value=" F 41 3 2"> F 41 3 2</option>
278 <option value=" I 4 3 2"> I 4 3 2</option>
279 <option value=" P 43 3 2"> P 43 3 2</option>
280 <option value=" P 41 3 2"> P 41 3 2</option>
281 <option value=" I 41 3 2"> I 41 3 2</option>
282 <option value=" P -4 3 M"> P -4 3 M</option>
283 <option value=" F 4 -3 M"> F 4 -3 M</option>
284 <option value=" I -4 3 M"> I -4 3 M</option>
285 <option value=" P -4 3 N"> P -4 3 N</option>
286 <option value=" F -4 3 C"> F -4 3 C</option>
287 <option value=" I -4 3 D"> I -4 3 D</option>
288 <option value=" P M -3 M"> P M -3 M</option>
289 <option value=" P N -3 N"> P N -3 N</option>
290 <option value=" P M -3 N"> P M -3 N</option>
291 <option value=" P N -3 M"> P N -3 M</option>
292 <option value=" F M -3 M"> F M -3 M</option>
293 <option value=" F M -3 C"> F M -3 C</option>
294 <option value=" F D -3 M"> F D -3 M</option>
295 <option value=" F D -3 C"> F D -3 C</option>
296 <option value=" I M -3 M"> I M -3 M</option>
297 <option value=" I A -3 D"> I A -3 D</option>
298 <option value=" B 2"> B 2</option>
299 <option value=" P 1 1 21"> P 1 1 21</option>
300 <option value=" P 2 21 21"> P 2 21 21</option>
301 <option value=" P 21 2 21"> P 21 2 21</option>
302 <option value=" I 1 2 1"> I 1 2 1</option>
303 </param>
304 <param name="param_axis_a" type="float" value="0.0" label="cell axis a" help="(-axis_a) "/>
305 <param name="param_axis_b" type="float" value="0.0" label="cell axis" help="(-axis_b) "/>
306 <param name="param_axis_c" type="float" value="0.0" label="cell axis c" help="(-axis_c) "/>
307 <param name="param_angle_alpha" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle alpha" help="(-angle_alpha) "/>
308 <param name="param_angle_beta" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle beta" help="(-angle_beta) "/>
309 <param name="param_angle_gamma" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle gamma" help="(-angle_gamma) "/>
310 <param name="param_from_uc_a" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index a" help="(-from_uc_a) "/>
311 <param name="param_from_uc_b" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index" help="(-from_uc_b) "/>
312 <param name="param_from_uc_c" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index c" help="(-from_uc_c) "/>
313 <param name="param_to_uc_a" type="integer" value="0" label="to unit cell index a" help="(-to_uc_a) "/>
314 <param name="param_to_uc_b" type="integer" value="0" label="to unit cell index" help="(-to_uc_b) "/>
315 <param name="param_to_uc_c" type="integer" value="0" label="to unit cell index c" help="(-to_uc_c) "/>
316 </inputs>
317 <expand macro="advanced_options"/>
318 <outputs>
319 <data name="param_o" format="pdb"/>
320 </outputs>
321 <help>TODO: Manual
322
323 </help>
324 </tool>