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comparison ob_convert.xml @ 7:a9df9aae60bb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:37:52 -0400
parents edb576416262
children a072cb207571
comparison
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6:37f6668ce540 7:a9df9aae60bb
1 <tool id="openbabel_compound_convert" name="Compound Convert" version="@VERSION@.0"> 1 <tool id="openbabel_compound_convert" name="Compound conversion" version="@VERSION@.0">
2 <description>Converts various chemistry and molecular modeling data files</description> 2 <description>- interconvert between 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> 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 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. 5 and run the job in non-multi mode.
6 --> 6 -->
7 <macros> 7 <macros>
218 <when value="c3d2" /> 218 <when value="c3d2" />
219 <when value="caccrt" /> 219 <when value="caccrt" />
220 <when value="cache" /> 220 <when value="cache" />
221 <when value="cacint" /> 221 <when value="cacint" />
222 <when value="can"> 222 <when value="can">
223 <param name="can_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> 223 <param name="can_exp_h" type="boolean" label="Explicitly include hydrogens in output (-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" /> 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" /> 225 <param name="can_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as 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" /> 226 <param name="can_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2]) (-xa)" truevalue="-xa" falsevalue="" checked="false" />
227 </when> 227 </when>
228 <when value="cdxml" /> 228 <when value="cdxml" />
229 <when value="cht" /> 229 <when value="cht" />
230 <when value="cif" /> 230 <when value="cif" />
231 <when value="cml"> 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" /> 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" /> 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" /> 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" /> 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" /> 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" /> 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" /> 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" /> 239 <param name="cml_properties" type="boolean" label="Write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
240 <expand macro="2D_3D_opts" /> 240 <expand macro="2D_3D_opts" />
241 </when> 241 </when>
242 <when value="cmlr" /> 242 <when value="cmlr" />
243 <when value="com" /> 243 <when value="com" />
244 <when value="copy" /> 244 <when value="copy" />
257 <option value="-xfFP2" selected="True">FP2</option> 257 <option value="-xfFP2" selected="True">FP2</option>
258 <option value="-xfFP3">FP3</option> 258 <option value="-xfFP3">FP3</option>
259 <option value="-xfFP4">FP4</option> 259 <option value="-xfFP4">FP4</option>
260 <option value="-xfMACCS">MACCS</option> 260 <option value="-xfMACCS">MACCS</option>
261 </param> 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"> 262 <param name="fpt_fold" type="integer" value="0" label="Fold fingerprint to the number of specified bits (32, 64, 128, etc.)" help="Use zero for default">
263 <validator type="in_range" min="0" /> 263 <validator type="in_range" min="0" />
264 </param> 264 </param>
265 <param name="fpt_hex_multiple" type="boolean" label="hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" /> 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" /> 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" /> 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" /> 268 <param name="fpt_unset" type="boolean" label="Describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" />
269 </when> 269 </when>
270 <when value="fract" /> 270 <when value="fract" />
271 <when value="fs"> 271 <when value="fs">
272 <param name="fs_fptype" type="select" label="Fingerprint type"> 272 <param name="fs_fptype" type="select" label="Fingerprint type">
273 <option value="-xfFP2" selected="True">FP2</option> 273 <option value="-xfFP2" selected="True">FP2</option>
274 <option value="-xfFP3">FP3</option> 274 <option value="-xfFP3">FP3</option>
275 <option value="-xfFP4">FP4</option> 275 <option value="-xfFP4">FP4</option>
276 <option value="-xfMACCS">MACCS</option> 276 <option value="-xfMACCS">MACCS</option>
277 </param> 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"> 278 <param name="fs_fold" type="integer" value="0" label="Fold fingerprint to the number of specified bits (32, 64, 128, etc.)" help="Use zero for default">
279 <validator type="in_range" min="0" /> 279 <validator type="in_range" min="0" />
280 </param> 280 </param>
281 </when> 281 </when>
282 <when value="gamin" /> 282 <when value="gamin" />
283 <when value="gau" /> 283 <when value="gau" />
284 <when value="gpr" /> 284 <when value="gpr" />
285 <when value="gr96" /> 285 <when value="gr96" />
286 <when value="hin" /> 286 <when value="hin" />
287 <when value="inchi"> 287 <when value="inchi">
288 <param name="inchi_key" type="boolean" label="output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" /> 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" /> 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" /> 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" /> 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"> 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> 293 <option value="/formula">formula only</option>
294 <option value="/connect">formula and connectivity only</option> 294 <option value="/connect">formula and connectivity only</option>
295 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> 295 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option>
296 <option value="/sp3">ignore sp3 stereochemistry</option> 296 <option value="/sp3">ignore sp3 stereochemistry</option>
297 <option value="/noEZ">ignore E/Z steroeochemistry</option> 297 <option value="/noEZ">ignore E/Z steroeochemistry</option>
319 <when value="inp" /> 319 <when value="inp" />
320 <when value="jin" /> 320 <when value="jin" />
321 <when value="mmd" /> 321 <when value="mmd" />
322 <when value="mmod" /> 322 <when value="mmod" />
323 <when value="mol2"> 323 <when value="mol2">
324 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands" help="(-xl)" 324 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands?" help="(-xl)"
325 truevalue="-xl" falsevalue="" checked="false" /> 325 truevalue="-xl" falsevalue="" checked="false" />
326 <expand macro="2D_3D_opts" /> 326 <expand macro="2D_3D_opts" />
327 </when> 327 </when>
328 <when value="molreport" /> 328 <when value="molreport" />
329 <when value="mop" /> 329 <when value="mop" />
340 <when value="qcin" /> 340 <when value="qcin" />
341 <when value="report" /> 341 <when value="report" />
342 <when value="rxn" /> 342 <when value="rxn" />
343 <when value="sdf"> 343 <when value="sdf">
344 <param name="sdf_exp_h" type="boolean" truevalue="-x3" falsevalue="" checked="false" 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)" /> 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" 346 <param name="sdf_no_prop" type="boolean" truevalue="-xm" falsevalue="" checked="false"
347 label="write no properties" help="(-xm)" /> 347 label="Do not write properties" help="(-xm)" />
348 <param name="sdf_wedge_bonds" type="boolean" truevalue="-xw" falsevalue="" checked="false" 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)"/> 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" 350 <param name="sdf_alias_out" type="boolean" truevalue="-xA" falsevalue="" checked="false"
351 label="output in Alias form, e.g. Ph" help="(-xA)" /> 351 label="Output in alias form, e.g. Ph for phenyl" help="(-xA)" />
352 <expand macro="2D_3D_opts" /> 352 <expand macro="2D_3D_opts" />
353 </when> 353 </when>
354 <when value="smi"> 354 <when value="smi">
355 <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such" help="(-xh)" 355 <param name="smi_exp_h" type="boolean" label="Explicitly include hydrogens in output" help="(-xh)"
356 truevalue="-xh" falsevalue="" checked="false" /> 356 truevalue="-xh" falsevalue="" checked="false" />
357 <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings" help="(-xi)" 357 <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings" help="(-xi)"
358 truevalue="-xi" falsevalue="" checked="false" /> 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" 359 <param name="smi_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc)" help="(-xr)" truevalue="-xr"
360 falsevalue="" checked="false" /> 360 falsevalue="" checked="false" />
361 <param name="smi_atomclass_out" type="boolean" label="Output atomclass like [C:2]" help="(-xa)" 361 <param name="smi_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2])" help="(-xa)"
362 truevalue="-xa" falsevalue="" checked="false" /> 362 truevalue="-xa" falsevalue="" checked="false" />
363 <param name="smi_can" type="boolean" label="Output in canonical form" help="(-xc)" 363 <param name="smi_can" type="boolean" label="Output in canonical form" help="(-xc)"
364 truevalue="-xc" falsevalue="" checked="false" /> 364 truevalue="-xc" falsevalue="" checked="false" />
365 <param name="smi_coordinates" type="boolean" label="append X/Y coordinates in canonical-SMILES order" help="(-xx)" 365 <param name="smi_coordinates" type="boolean" label="Append X/Y coordinates in canonical-SMILES order" help="(-xx)"
366 truevalue="-xx" falsevalue="" checked="false" /> 366 truevalue="-xx" falsevalue="" checked="false" />
367 </when> 367 </when>
368 <when value="tdd" /> 368 <when value="tdd" />
369 <when value="test" /> 369 <when value="test" />
370 <when value="therm" /> 370 <when value="therm" />
378 <when value="zin" /> 378 <when value="zin" />
379 </conditional> 379 </conditional>
380 380
381 <!-- Options for all formats.--> 381 <!-- Options for all formats.-->
382 <param name="remove_h" type="boolean" truevalue="-d" falsevalue="" 382 <param name="remove_h" type="boolean" truevalue="-d" falsevalue=""
383 label="Delete hydrogen atoms, make all hydrogen implicit" help="(-d)" /> 383 label="Delete hydrogen atoms, make all hydrogens implicit" help="(-d)" />
384 <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/> 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="" 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)" /> 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"/> 387 <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/>
388 388
389 <!-- Uniqueness --> 389 <!-- Uniqueness -->
390 <conditional name="unique"> 390 <conditional name="unique">
391 <param name="unique_opts_selector" type="select" label="Uniqueness according to"> 391 <param name="unique_opts_selector" type="select" label="Uniqueness according to">
392 <option value="" selected="True">No unique filter</option> 392 <option value="" selected="True">No unique filter</option>
393 <option value="inchi">InChI</option> 393 <option value="inchi">InChI</option>
394 <option value="cansmi">canonical SMILES with stereochemical information</option> 394 <option value="cansmi">Canonical SMILES with stereochemical information</option>
395 <option value="cansmiNS">canonical SMILES without stereochemical information</option> 395 <option value="cansmiNS">Canonical SMILES without stereochemical information</option>
396 <option value="title">title</option> 396 <option value="title">Title</option>
397 </param> 397 </param>
398 <when value="" /> 398 <when value="" />
399 <when value="cansmi" /> 399 <when value="cansmi" />
400 <when value="cansmiNS" /> 400 <when value="cansmiNS" />
401 <when value="title" /> 401 <when value="title" />
468 468
469 .. class:: infomark 469 .. class:: infomark
470 470
471 **What this tool does** 471 **What this tool does**
472 472
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. 473 The compound converter combines several Open Babel command prompt converters into a single easy-to-use tool. It interconverts various chemistry and molecular modeling data files. The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) while others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI).
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).
476 474
477 ----- 475 -----
478 476
479 .. class:: infomark 477 .. class:: infomark
480 478