Mercurial > repos > bgruening > openbabel_compound_convert
comparison ob_convert.xml @ 0:edb576416262 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author | bgruening |
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date | Sat, 20 May 2017 08:37:48 -0400 |
parents | |
children | a9df9aae60bb |
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1 <tool id="openbabel_compound_convert" name="Compound Convert" version="@VERSION@.0"> | |
2 <description>Converts various chemistry and molecular modeling data files</description> | |
3 <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | |
4 We can't use that currently, because a few output-datatypes, like the fastsearch index do not support merging. We need to patch galaxy to not abort in such a case | |
5 and run the job in non-multi mode. | |
6 --> | |
7 <macros> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="requirements"/> | |
11 <command detect_errors="aggressive"> | |
12 <![CDATA[ | |
13 | |
14 #set $format = $oformat.oformat_opts_selector | |
15 | |
16 #if $format == "fs": | |
17 ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs. | |
18 ## Because openbabel likes file extensions, we give the molecule file a proper file extension. | |
19 mkdir $outfile.files_path; | |
20 cp "${infile}" ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )}; | |
21 #end if | |
22 | |
23 obabel -i "${infile.ext}" | |
24 | |
25 #if $format == "fs": | |
26 ## the fs filetype need his own symlink path, all others can take the original ones | |
27 ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )} | |
28 -o "$format" -e | |
29 -O ${os.path.join($outfile.files_path,'molecule.fs')} | |
30 #if int($oformat.fs_fold) > 0: | |
31 -xN$oformat.fs_fold | |
32 #end if | |
33 ${oformat.fs_fptype} | |
34 #else: | |
35 "${infile}" | |
36 -o "${format}" | |
37 -O "${outfile}" | |
38 -e | |
39 #end if | |
40 | |
41 #if $format == 'cml': | |
42 $oformat.cml_array | |
43 $oformat.cml_cml1 | |
44 $oformat.cml_aromatic | |
45 $oformat.cml_hydrogen | |
46 $oformat.cml_metadata | |
47 $oformat.cml_omit | |
48 $oformat.cml_continuous | |
49 $oformat.cml_properties | |
50 $oformat.gen2d | |
51 $oformat.gen3d | |
52 #elif $format == 'inchi': | |
53 ## Ignore less import warnings | |
54 -w | |
55 #if $oformat.inchi_truncate: | |
56 #set $truncate = ''.join( str( $oformat.inchi_truncate ).split( ',' ) ) | |
57 -xT ${truncate} | |
58 #end if | |
59 | |
60 #if $oformat.inchi_additional: | |
61 #set $additional = ' '.join( str( $oformat.inchi_additional ).split( ',' ) ) | |
62 -xX '${additional}' | |
63 #end if | |
64 | |
65 $oformat.inchi_key | |
66 $oformat.inchi_name | |
67 $oformat.inchi_unique | |
68 $oformat.inchi_unique_sort | |
69 #elif $format == 'can': | |
70 $oformat.can_exp_h | |
71 $oformat.can_iso_chi | |
72 $oformat.can_rad | |
73 $oformat.can_atomclass_out | |
74 #elif $format == 'smi': | |
75 $oformat.smi_exp_h | |
76 $oformat.smi_iso_chi | |
77 $oformat.smi_rad | |
78 $oformat.smi_atomclass_out | |
79 $oformat.smi_can | |
80 $oformat.smi_coordinates | |
81 #elif $format == 'sdf': | |
82 $oformat.sdf_exp_h | |
83 $oformat.sdf_no_prop | |
84 $oformat.sdf_wedge_bonds | |
85 $oformat.sdf_alias_out | |
86 $oformat.gen2d | |
87 $oformat.gen3d | |
88 #elif $format == 'fpt': | |
89 $oformat.fpt_fptype | |
90 #if int($oformat.fpt_fold) > 0: | |
91 $oformat.fpt_fold | |
92 #end if | |
93 $oformat.fpt_hex_multiple | |
94 $oformat.fpt_hex | |
95 $oformat.fpt_set | |
96 $oformat.fpt_unset | |
97 #elif $format == 'mol2': | |
98 $oformat.mol2_ignore_res | |
99 $oformat.gen2d | |
100 $oformat.gen3d | |
101 #end if | |
102 | |
103 ## Uniqueness according to stripped InChI's or canonical SMILES | |
104 #if str($unique.unique_opts_selector): | |
105 #if $unique.unique_opts_selector == 'inchi': | |
106 #if $unique.truncate: | |
107 #set $truncate = ''.join( str( $unique.truncate ).split( ',' ) ) | |
108 --unique $truncate | |
109 #end if | |
110 #else | |
111 --unique $unique.unique_opts_selector | |
112 #end if | |
113 #end if | |
114 | |
115 #if str($appendtotitle).strip(): | |
116 --addtotitle '${appendtotitle}' | |
117 #end if | |
118 | |
119 $remove_h | |
120 $dative_bonds | |
121 | |
122 #if float($ph) >= 0: | |
123 -p $ph | |
124 #end if | |
125 | |
126 ]]> | |
127 </command> | |
128 <inputs> | |
129 <expand macro="infile_all_types"/> | |
130 <conditional name="oformat"> | |
131 <param name="oformat_opts_selector" type="select" label="Output format"> | |
132 <option value="acr">Carine ASCI Crystal</option> | |
133 <option value="alc">Alchemy format</option> | |
134 <option value="bgf">MSI BGF format</option> | |
135 <option value="box">Dock 3.5 Box format</option> | |
136 <option value="bs">Ball and Stick format</option> | |
137 <option value="c3d1">Chem3D Cartesian 1 format</option> | |
138 <option value="c3d2">Chem3D Cartesian 2 format</option> | |
139 <option value="caccrt">Cacao Cartesian format</option> | |
140 <option value="cache">CAChe MolStruct format</option> | |
141 <option value="cacint">Cacao Internal format</option> | |
142 <option value="can" selected="True">Canonical SMILES format (can)</option> | |
143 <option value="cdxml">ChemDraw CDXML format</option> | |
144 <option value="cht">Chemtool format</option> | |
145 <option value="cif">Crystallographic Information File</option> | |
146 <option value="cml">Chemical Markup Language (CML)</option> | |
147 <option value="cmlr">CML Reaction format</option> | |
148 <option value="com">Gaussian 98/03 Cartesian Input</option> | |
149 <option value="copy">Copies raw text</option> | |
150 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> | |
151 <option value="crk3d">Chemical Resource Kit 3D format</option> | |
152 <option value="csr">Accelrys/MSI Quanta CSR format</option> | |
153 <option value="cssr">CSD CSSR format</option> | |
154 <option value="ct">ChemDraw Connection Table format</option> | |
155 <option value="dmol">DMol3 coordinates format</option> | |
156 <!--<option value="ent">Protein Data Bank format</option> | |
157 <option value="fa">FASTA format</option>--> | |
158 <option value="fasta">FASTA format</option> | |
159 <option value="feat">Feature format</option> | |
160 <option value="fh">Fenske-Hall Z-Matrix format</option> | |
161 <option value="fix">SMILES FIX format</option> | |
162 <option value="fpt">Fingerprint format (fpt)</option> | |
163 <option value="fract">Free Form Fractional format</option> | |
164 <option value="fs">Open Babel FastSearching database (fs)</option> | |
165 <!--<option value="fsa">FASTA format</option>--> | |
166 <option value="gamin">GAMESS Input</option> | |
167 <option value="gau">Gaussian 98/03 Cartesian Input</option> | |
168 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option> | |
169 <option value="gjf">Gaussian 98/03 Cartesian Input</option>--> | |
170 <option value="gpr">Ghemical format</option> | |
171 <option value="gr96">GROMOS96 format</option> | |
172 <option value="hin">HyperChem HIN format</option> | |
173 <option value="inchi">IUPAC InChI</option> | |
174 <option value="inp">GAMESS Input</option> | |
175 <option value="jin">Jaguar input format</option> | |
176 <!--<option value="mdl">MDL MOL format (mol)</option>--> | |
177 <option value="mmd">MacroModel format</option> | |
178 <option value="mmod">MacroModel format</option> | |
179 <!--<option value="mol">MDL MOL format (mol)</option> use SDF--> | |
180 <option value="mol2">Sybyl Mol2 format (mol2)</option> | |
181 <option value="molreport">Open Babel molecule report</option> | |
182 <option value="mop">MOPAC Cartesian format</option> | |
183 <option value="mopcrt">MOPAC Cartesian format</option> | |
184 <option value="mopin">MOPAC Internal</option> | |
185 <option value="mpc">MOPAC Cartesian format</option> | |
186 <option value="mpd">Sybyl descriptor format</option> | |
187 <option value="mpqcin">MPQC simplified input format</option> | |
188 <option value="nw">NWChem input format</option> | |
189 <option value="pcm">PCModel format</option> | |
190 <option value="pdb">Protein Data Bank format (pdb)</option> | |
191 <option value="pov">POV-Ray input format</option> | |
192 <option value="pqs">Parallel Quantum Solutions format</option> | |
193 <option value="qcin">Q-Chem input format</option> | |
194 <option value="report">Open Babel report format</option> | |
195 <option value="rxn">MDL RXN format</option> | |
196 <!--<option value="sd">MDL MOL format</option>--> | |
197 <option value="sdf">MDL MOL format (sdf, mol)</option> | |
198 <option value="smi">SMILES format (smi)</option> | |
199 <!--<option value="sy2">Sybyl Mol2 format</option>--> | |
200 <option value="tdd">Thermo format</option> | |
201 <option value="test">Test format</option> | |
202 <option value="therm">Thermo format</option> | |
203 <option value="tmol">TurboMole Coordinate format</option> | |
204 <option value="txyz">Tinker MM2 format</option> | |
205 <option value="unixyz">UniChem XYZ format</option> | |
206 <option value="vmol">ViewMol format</option> | |
207 <option value="xed">XED format</option> | |
208 <option value="xyz">XYZ cartesian coordinates format</option> | |
209 <option value="yob">YASARA.org YOB format</option> | |
210 <option value="zin">ZINDO input format</option> | |
211 </param> | |
212 <when value="acr" /> | |
213 <when value="alc" /> | |
214 <when value="bgf" /> | |
215 <when value="box" /> | |
216 <when value="bs" /> | |
217 <when value="c3d1" /> | |
218 <when value="c3d2" /> | |
219 <when value="caccrt" /> | |
220 <when value="cache" /> | |
221 <when value="cacint" /> | |
222 <when value="can"> | |
223 <param name="can_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
224 <param name="can_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" /> | |
225 <param name="can_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" /> | |
226 <param name="can_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" /> | |
227 </when> | |
228 <when value="cdxml" /> | |
229 <when value="cht" /> | |
230 <when value="cif" /> | |
231 <when value="cml"> | |
232 <param name="cml_cml1" type="boolean" label="convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" /> | |
233 <param name="cml_array" type="boolean" label="write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" /> | |
234 <param name="cml_aromatic" type="boolean" label="write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" /> | |
235 <param name="cml_hydrogen" type="boolean" label="use hydrogen Count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
236 <param name="cml_metadata" type="boolean" label="write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" /> | |
237 <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" /> | |
238 <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" /> | |
239 <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" /> | |
240 <expand macro="2D_3D_opts" /> | |
241 </when> | |
242 <when value="cmlr" /> | |
243 <when value="com" /> | |
244 <when value="copy" /> | |
245 <when value="crk2d" /> | |
246 <when value="crk3d" /> | |
247 <when value="csr" /> | |
248 <when value="cssr" /> | |
249 <when value="ct" /> | |
250 <when value="dmol" /> | |
251 <when value="fasta" /> | |
252 <when value="feat" /> | |
253 <when value="fh" /> | |
254 <when value="fix" /> | |
255 <when value="fpt"> | |
256 <param name="fpt_fptype" type="select" label="Fingerprint type"> | |
257 <option value="-xfFP2" selected="True">FP2</option> | |
258 <option value="-xfFP3">FP3</option> | |
259 <option value="-xfFP4">FP4</option> | |
260 <option value="-xfMACCS">MACCS</option> | |
261 </param> | |
262 <param name="fpt_fold" type="integer" value="0" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default"> | |
263 <validator type="in_range" min="0" /> | |
264 </param> | |
265 <param name="fpt_hex_multiple" type="boolean" label="hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
266 <param name="fpt_hex" type="boolean" label="hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" /> | |
267 <param name="fpt_set" type="boolean" label="describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" /> | |
268 <param name="fpt_unset" type="boolean" label="describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" /> | |
269 </when> | |
270 <when value="fract" /> | |
271 <when value="fs"> | |
272 <param name="fs_fptype" type="select" label="Fingerprint type"> | |
273 <option value="-xfFP2" selected="True">FP2</option> | |
274 <option value="-xfFP3">FP3</option> | |
275 <option value="-xfFP4">FP4</option> | |
276 <option value="-xfMACCS">MACCS</option> | |
277 </param> | |
278 <param name="fs_fold" type="integer" value="0" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default"> | |
279 <validator type="in_range" min="0" /> | |
280 </param> | |
281 </when> | |
282 <when value="gamin" /> | |
283 <when value="gau" /> | |
284 <when value="gpr" /> | |
285 <when value="gr96" /> | |
286 <when value="hin" /> | |
287 <when value="inchi"> | |
288 <param name="inchi_key" type="boolean" label="output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" /> | |
289 <param name="inchi_name" type="boolean" label="add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" /> | |
290 <param name="inchi_unique" type="boolean" label="output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" /> | |
291 <param name="inchi_unique_sort" type="boolean" label="output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" /> | |
292 <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="truncate InChI according to various parameters"> | |
293 <option value="/formula">formula only</option> | |
294 <option value="/connect">formula and connectivity only</option> | |
295 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> | |
296 <option value="/sp3">ignore sp3 stereochemistry</option> | |
297 <option value="/noEZ">ignore E/Z steroeochemistry</option> | |
298 <option value="/nochg">ignore charge and protonation</option> | |
299 <option value="/noiso">ignore isotopes</option> | |
300 </param> | |
301 | |
302 <param name="inchi_additional" type="select" multiple="True" display="checkboxes" label="Additional InChI options" help="For more information please see the InChI documentation (http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html)."> | |
303 <option value="NEWPSOFF">Narrow End of Wedge Points to Stereo is OFF (NEWPSOFF - stdInChI)</option> | |
304 <option value="DoNotAddH">Skip the addition of hydrogen atoms (DoNotAddH - stdInChI)</option> | |
305 <option value="SNon">Exclude stereo (SNon - stdInChI)</option> | |
306 <option value="SRel">Relative stereo (SRel)</option> | |
307 <option value="SRac">Racemic stereo (SRac)</option> | |
308 <option value="SUCF">Use Chiral Flag (SUCF)</option> | |
309 <option value="ChiralFlagON">Set Chiral Flag (ChrialFlagON)</option> | |
310 <option value="ChiralFlagOFF">Set Not-Chiral Flag (ChrialFlagOFF)</option> | |
311 <option value="SUU">Include omitted unknown/undefined stereo (SUU)</option> | |
312 <option value="SLUUD">Stereo labels for "unknown" and "undefined" are different, 'u' and '?', respectively (SLUUD) </option> | |
313 <option value="FixedH">Mobile H Perception Off (FixedH)</option> | |
314 <option value="RecMet">Include reconnected bond to metal results (RecMet)</option> | |
315 <option value="KET">Keto-enol tautomerism (KET)</option> | |
316 <option value="15T">1,5-tautomerism (15T)</option> | |
317 </param> | |
318 </when> | |
319 <when value="inp" /> | |
320 <when value="jin" /> | |
321 <when value="mmd" /> | |
322 <when value="mmod" /> | |
323 <when value="mol2"> | |
324 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands" help="(-xl)" | |
325 truevalue="-xl" falsevalue="" checked="false" /> | |
326 <expand macro="2D_3D_opts" /> | |
327 </when> | |
328 <when value="molreport" /> | |
329 <when value="mop" /> | |
330 <when value="mopcrt" /> | |
331 <when value="mopin" /> | |
332 <when value="mpc" /> | |
333 <when value="mpd" /> | |
334 <when value="mpqcin" /> | |
335 <when value="nw" /> | |
336 <when value="pcm" /> | |
337 <when value="pdb" /> | |
338 <when value="pov" /> | |
339 <when value="pqs" /> | |
340 <when value="qcin" /> | |
341 <when value="report" /> | |
342 <when value="rxn" /> | |
343 <when value="sdf"> | |
344 <param name="sdf_exp_h" type="boolean" truevalue="-x3" falsevalue="" checked="false" | |
345 label="output V3000 not V2000 (used for >999 atoms/bonds)" help="(-x3)" /> | |
346 <param name="sdf_no_prop" type="boolean" truevalue="-xm" falsevalue="" checked="false" | |
347 label="write no properties" help="(-xm)" /> | |
348 <param name="sdf_wedge_bonds" type="boolean" truevalue="-xw" falsevalue="" checked="false" | |
349 label="use wedge and hash bonds from input (2D structures only)" help="(-xw)"/> | |
350 <param name="sdf_alias_out" type="boolean" truevalue="-xA" falsevalue="" checked="false" | |
351 label="output in Alias form, e.g. Ph" help="(-xA)" /> | |
352 <expand macro="2D_3D_opts" /> | |
353 </when> | |
354 <when value="smi"> | |
355 <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such" help="(-xh)" | |
356 truevalue="-xh" falsevalue="" checked="false" /> | |
357 <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings" help="(-xi)" | |
358 truevalue="-xi" falsevalue="" checked="false" /> | |
359 <param name="smi_rad" type="boolean" label="Radicals lower case eg ethyl is Cc" help="(-xr)" truevalue="-xr" | |
360 falsevalue="" checked="false" /> | |
361 <param name="smi_atomclass_out" type="boolean" label="Output atomclass like [C:2]" help="(-xa)" | |
362 truevalue="-xa" falsevalue="" checked="false" /> | |
363 <param name="smi_can" type="boolean" label="Output in canonical form" help="(-xc)" | |
364 truevalue="-xc" falsevalue="" checked="false" /> | |
365 <param name="smi_coordinates" type="boolean" label="append X/Y coordinates in canonical-SMILES order" help="(-xx)" | |
366 truevalue="-xx" falsevalue="" checked="false" /> | |
367 </when> | |
368 <when value="tdd" /> | |
369 <when value="test" /> | |
370 <when value="therm" /> | |
371 <when value="tmol" /> | |
372 <when value="txyz" /> | |
373 <when value="unixyz" /> | |
374 <when value="vmol" /> | |
375 <when value="xed" /> | |
376 <when value="xyz" /> | |
377 <when value="yob" /> | |
378 <when value="zin" /> | |
379 </conditional> | |
380 | |
381 <!-- Options for all formats.--> | |
382 <param name="remove_h" type="boolean" truevalue="-d" falsevalue="" | |
383 label="Delete hydrogen atoms, make all hydrogen implicit" help="(-d)" /> | |
384 <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/> | |
385 <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue="" | |
386 label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" /> | |
387 <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/> | |
388 | |
389 <!-- Uniqueness --> | |
390 <conditional name="unique"> | |
391 <param name="unique_opts_selector" type="select" label="Uniqueness according to"> | |
392 <option value="" selected="True">No unique filter</option> | |
393 <option value="inchi">InChI</option> | |
394 <option value="cansmi">canonical SMILES with stereochemical information</option> | |
395 <option value="cansmiNS">canonical SMILES without stereochemical information</option> | |
396 <option value="title">title</option> | |
397 </param> | |
398 <when value="" /> | |
399 <when value="cansmi" /> | |
400 <when value="cansmiNS" /> | |
401 <when value="title" /> | |
402 <when value="inchi"> | |
403 <param name="truncate" type="select" multiple="True" display="checkboxes" label="Uniqueness defined as truncated InChI"> | |
404 <option value="/formula">formula only</option> | |
405 <option value="/connect">formula and connectivity only</option> | |
406 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> | |
407 <option value="/sp3">ignore sp3 stereochemistry</option> | |
408 <option value="/noEZ">ignore E/Z steroeochemistry</option> | |
409 <option value="/nochg">ignore charge and protonation</option> | |
410 <option value="/noiso">ignore isotopes</option> | |
411 </param> | |
412 </when> | |
413 </conditional> | |
414 </inputs> | |
415 | |
416 <outputs> | |
417 <data name="outfile" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}"> | |
418 <change_format> | |
419 <when input="oformat.oformat_opts_selector" value="sdf" format="sdf"/> | |
420 <when input="oformat.oformat_opts_selector" value="can" format="smi"/> | |
421 <when input="oformat.oformat_opts_selector" value="smi" format="smi"/> | |
422 <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/> | |
423 <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/> | |
424 <when input="oformat.oformat_opts_selector" value="cml" format="cml"/> | |
425 <when input="oformat.oformat_opts_selector" value="mol" format="mol"/> | |
426 <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/> | |
427 <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/> | |
428 </change_format> | |
429 </data> | |
430 </outputs> | |
431 <tests> | |
432 <test> | |
433 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | |
434 <param name="oformat_opts_selector" value="cml" /> | |
435 <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" /> | |
436 </test> | |
437 <test> | |
438 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | |
439 <param name="oformat_opts_selector" value="fs" /> | |
440 <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs"> | |
441 <extra_files type="file" value="molecule.sdf" name="molecule.sdf" /> | |
442 <extra_files type="file" value="molecule.fs" name="molecule.fs" compare="sim_size" /> | |
443 </output> | |
444 </test> | |
445 <test> | |
446 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | |
447 <param name="oformat_opts_selector" value="inchi" /> | |
448 <output name="outfile" ftype="inchi" file="ob_convert_on_CID2244.inchi" /> | |
449 </test> | |
450 <test> | |
451 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | |
452 <param name="oformat_opts_selector" value="pdb" /> | |
453 <output name="outfile" ftype="pdb" file="ob_convert_on_CID2244.pdb" lines_diff="4" /> | |
454 </test> | |
455 <test> | |
456 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | |
457 <param name="oformat_opts_selector" value="can" /> | |
458 <output name="outfile" ftype="smi" file="ob_convert_on_CID2244.smi" /> | |
459 </test> | |
460 <test> | |
461 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | |
462 <param name="oformat_opts_selector" value="sdf" /> | |
463 <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/> | |
464 </test> | |
465 </tests> | |
466 <help> | |
467 <![CDATA[ | |
468 | |
469 .. class:: infomark | |
470 | |
471 **What this tool does** | |
472 | |
473 The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. | |
474 The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) | |
475 others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). | |
476 | |
477 ----- | |
478 | |
479 .. class:: infomark | |
480 | |
481 **Output** | |
482 | |
483 Can be specified manually. | |
484 | |
485 | |
486 ]]> | |
487 </help> | |
488 <expand macro="citations"/> | |
489 </tool> |