Mercurial > repos > bgruening > openbabel
annotate convert/ob_convert.xml @ 22:b4ba90dcfde0 default tip
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Tue, 23 Jul 2013 19:00:18 +0200 |
| parents | c09a44237bd5 |
| children |
| rev | line source |
|---|---|
|
15
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
14
diff
changeset
|
1 <tool id="ctb_compound_convert" name="Compound Convert" version="0.1"> |
| 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 | |
|
15
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
14
diff
changeset
|
5 and run the job in non-multi mode. |
| 0 | 6 --> |
| 7 <requirements> | |
| 8 <requirement type="package" version="2.3.2">openbabel</requirement> | |
| 9 </requirements> | |
| 10 <command> | |
| 11 ## The command is a Cheetah template which allows some Python based syntax. | |
| 12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
| 13 | |
| 7 | 14 #set $format = $oformat.oformat_opts_selector |
| 15 | |
| 16 #if $format == "fs": | |
| 0 | 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 $outfile.extra_files_path; | |
| 20 cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}; | |
| 21 #end if | |
| 22 | |
| 23 obabel -i "${infile.ext}" | |
| 7 | 24 |
| 25 #if $format == "fs": | |
| 26 ## the fs filetype need his own symlink path, all others can take the original ones | |
| 0 | 27 ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )} |
| 7 | 28 -o "$format" -e |
| 0 | 29 -O ${os.path.join($outfile.extra_files_path,'molecule.fs')} |
| 7 | 30 #if int($oformat.fs_fold) > 0: |
| 10 | 31 -xN$oformat.fs_fold |
| 7 | 32 #end if |
| 10 | 33 ${oformat.fs_fptype} |
| 0 | 34 #else: |
| 35 "${infile}" | |
| 7 | 36 -o "$format" |
| 0 | 37 -O "${outfile}" |
| 7 | 38 -e |
| 39 #end if | |
| 40 | |
| 41 | |
| 42 #if $format == 'cml': | |
| 43 $oformat.cml_array | |
| 44 $oformat.cml_cml1 | |
| 45 $oformat.cml_aromatic | |
| 46 $oformat.cml_hydrogen | |
| 47 $oformat.cml_metadata | |
| 48 $oformat.cml_omit | |
| 49 $oformat.cml_continuous | |
| 50 $oformat.cml_properties | |
| 9 | 51 $oformat.cml_gen2d |
| 52 $oformat.cml_gen3d | |
| 7 | 53 #elif $format == 'inchi': |
| 54 ##ignore less import warnings | |
| 55 -w | |
| 56 #if $oformat.inchi_truncate: | |
| 57 #set $truncate = ''.join( str( $oformat.inchi_truncate ).split( ',' ) ) | |
| 58 -xT ${truncate} | |
| 59 #end if | |
| 60 | |
| 61 #if $oformat.inchi_additional: | |
| 62 #set $additional = ' '.join( str( $oformat.inchi_additional ).split( ',' ) ) | |
| 63 -xX '${additional}' | |
| 64 #end if | |
| 65 | |
| 66 $oformat.inchi_key | |
| 67 $oformat.inchi_name | |
| 68 $oformat.inchi_unique | |
| 69 $oformat.inchi_unique_sort | |
| 70 #elif $format == 'can': | |
| 71 $oformat.can_exp_h | |
| 72 $oformat.can_iso_chi | |
| 73 $oformat.can_rad | |
| 74 $oformat.can_atomclass_out | |
| 75 #elif $format == 'smi': | |
| 76 $oformat.smi_exp_h | |
| 77 $oformat.smi_iso_chi | |
| 78 $oformat.smi_rad | |
| 79 $oformat.smi_atomclass_out | |
| 80 $oformat.smi_can | |
| 81 $oformat.smi_coordinates | |
| 82 #elif $format == 'sdf': | |
| 83 $oformat.sdf_exp_h | |
| 84 $oformat.sdf_no_prop | |
| 85 $oformat.sdf_wedge_bonds | |
| 86 $oformat.sdf_alias_out | |
| 9 | 87 $oformat.sdf_gen2d |
| 88 $oformat.sdf_gen3d | |
| 7 | 89 #elif $format == 'fpt': |
| 90 $oformat.fpt_fptype | |
| 91 #if int($oformat.fpt_fold) > 0: | |
| 92 $oformat.fpt_fold | |
| 93 #end if | |
| 94 $oformat.fpt_hex_multiple | |
| 95 $oformat.fpt_hex | |
| 96 $oformat.fpt_set | |
| 97 $oformat.fpt_unset | |
| 98 #elif $format == 'mol2': | |
| 99 $oformat.mol2_ignore_res | |
| 9 | 100 $oformat.mol2_gen2d |
| 101 $oformat.mol2_gen3d | |
| 7 | 102 #end if |
| 103 | |
| 104 ## Uniqueness according to stripped InChI's or canonical SMILES | |
| 105 #if str($unique.unique_opts_selector): | |
| 106 #if $unique.unique_opts_selector == 'inchi': | |
| 107 #if $unique.truncate: | |
| 108 #set $truncate = ''.join( str( $unique.truncate ).split( ',' ) ) | |
| 109 --unique $truncate | |
| 110 #end if | |
| 111 #else | |
| 112 --unique $unique.unique_opts_selector | |
| 113 #end if | |
| 114 #end if | |
| 115 | |
| 116 | |
| 117 #if str($appendtotitle).strip(): | |
| 118 --addtotitle '${appendtotitle}' | |
| 0 | 119 #end if |
| 120 | |
| 121 $remove_h | |
| 7 | 122 $dative_bonds |
| 123 | |
| 0 | 124 #if int($ph) >= 0: |
| 125 -p $ph | |
| 126 #end if | |
| 7 | 127 |
| 0 | 128 2>&1 |
| 129 </command> | |
| 130 <inputs> | |
| 131 <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/> | |
| 7 | 132 <conditional name="oformat"> |
| 133 <param name="oformat_opts_selector" type="select" label="Output format"> | |
| 134 <option value="acr">Carine ASCI Crystal</option> | |
| 135 <option value="alc">Alchemy format</option> | |
| 136 <option value="bgf">MSI BGF format</option> | |
| 137 <option value="box">Dock 3.5 Box format</option> | |
| 138 <option value="bs">Ball and Stick format</option> | |
| 139 <option value="c3d1">Chem3D Cartesian 1 format</option> | |
| 140 <option value="c3d2">Chem3D Cartesian 2 format</option> | |
| 141 <option value="caccrt">Cacao Cartesian format</option> | |
| 142 <option value="cache">CAChe MolStruct format</option> | |
| 143 <option value="cacint">Cacao Internal format</option> | |
| 144 <option value="can" selected="True">Canonical SMILES format (can)</option> | |
| 145 <option value="cdxml">ChemDraw CDXML format</option> | |
| 146 <option value="cht">Chemtool format</option> | |
| 147 <option value="cif">Crystallographic Information File</option> | |
| 148 <option value="cml">Chemical Markup Language</option> | |
| 149 <option value="cmlr">CML Reaction format</option> | |
| 150 <option value="com">Gaussian 98/03 Cartesian Input</option> | |
| 151 <option value="copy">Copies raw text</option> | |
| 152 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> | |
| 153 <option value="crk3d">Chemical Resource Kit 3D format</option> | |
| 154 <option value="csr">Accelrys/MSI Quanta CSR format</option> | |
| 155 <option value="cssr">CSD CSSR format</option> | |
| 156 <option value="ct">ChemDraw Connection Table format</option> | |
| 157 <option value="dmol">DMol3 coordinates format</option> | |
| 158 <!--<option value="ent">Protein Data Bank format</option> | |
| 159 <option value="fa">FASTA format</option>--> | |
| 160 <option value="fasta">FASTA format</option> | |
| 161 <option value="feat">Feature format</option> | |
| 162 <option value="fh">Fenske-Hall Z-Matrix format</option> | |
| 163 <option value="fix">SMILES FIX format</option> | |
| 164 <option value="fpt">Fingerprint format (fpt)</option> | |
| 165 <option value="fract">Free Form Fractional format</option> | |
| 166 <option value="fs">Open Babel FastSearching database (fs)</option> | |
| 167 <!--<option value="fsa">FASTA format</option>--> | |
| 168 <option value="gamin">GAMESS Input</option> | |
| 169 <option value="gau">Gaussian 98/03 Cartesian Input</option> | |
| 170 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option> | |
| 171 <option value="gjf">Gaussian 98/03 Cartesian Input</option>--> | |
| 172 <option value="gpr">Ghemical format</option> | |
| 173 <option value="gr96">GROMOS96 format</option> | |
| 174 <option value="hin">HyperChem HIN format</option> | |
| 175 <option value="inchi">IUPAC InChI</option> | |
| 176 <option value="inp">GAMESS Input</option> | |
| 177 <option value="jin">Jaguar input format</option> | |
| 178 <!--<option value="mdl">MDL MOL format (mol)</option>--> | |
| 179 <option value="mmd">MacroModel format</option> | |
| 180 <option value="mmod">MacroModel format</option> | |
| 181 <!--<option value="mol">MDL MOL format (mol)</option> use SDF--> | |
| 182 <option value="mol2">Sybyl Mol2 format (mol2)</option> | |
| 183 <option value="molreport">Open Babel molecule report</option> | |
| 184 <option value="mop">MOPAC Cartesian format</option> | |
| 185 <option value="mopcrt">MOPAC Cartesian format</option> | |
| 186 <option value="mopin">MOPAC Internal</option> | |
| 187 <option value="mpc">MOPAC Cartesian format</option> | |
| 188 <option value="mpd">Sybyl descriptor format</option> | |
| 189 <option value="mpqcin">MPQC simplified input format</option> | |
| 190 <option value="nw">NWChem input format</option> | |
| 191 <option value="pcm">PCModel format</option> | |
| 192 <option value="pdb">Protein Data Bank format (pdb)</option> | |
| 193 <option value="pov">POV-Ray input format</option> | |
| 194 <option value="pqs">Parallel Quantum Solutions format</option> | |
| 195 <option value="qcin">Q-Chem input format</option> | |
| 196 <option value="report">Open Babel report format</option> | |
| 197 <option value="rxn">MDL RXN format</option> | |
| 198 <!--<option value="sd">MDL MOL format</option>--> | |
| 199 <option value="sdf">MDL MOL format (sdf, mol)</option> | |
| 200 <option value="smi">SMILES format (smi)</option> | |
| 201 <!--<option value="sy2">Sybyl Mol2 format</option>--> | |
| 202 <option value="tdd">Thermo format</option> | |
| 203 <option value="test">Test format</option> | |
| 204 <option value="therm">Thermo format</option> | |
| 205 <option value="tmol">TurboMole Coordinate format</option> | |
| 206 <option value="txyz">Tinker MM2 format</option> | |
| 207 <option value="unixyz">UniChem XYZ format</option> | |
| 208 <option value="vmol">ViewMol format</option> | |
| 209 <option value="xed">XED format</option> | |
| 210 <option value="xyz">XYZ cartesian coordinates format</option> | |
| 211 <option value="yob">YASARA.org YOB format</option> | |
| 212 <option value="zin">ZINDO input format</option> | |
| 213 </param> | |
| 214 <when value="acr" /> | |
| 215 <when value="alc" /> | |
| 216 <when value="bgf" /> | |
| 217 <when value="box" /> | |
| 218 <when value="bs" /> | |
| 219 <when value="c3d1" /> | |
| 220 <when value="c3d2" /> | |
| 221 <when value="caccrt" /> | |
| 222 <when value="cache" /> | |
| 223 <when value="cacint" /> | |
| 224 <when value="can"> | |
| 225 <param name="can_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
| 226 <param name="can_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" /> | |
| 227 <param name="can_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" /> | |
| 228 <param name="can_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" /> | |
| 229 </when> | |
| 230 <when value="cdxml" /> | |
| 231 <when value="cht" /> | |
| 232 <when value="cif" /> | |
| 233 <when value="cml"> | |
| 234 <param name="cml_cml1" type="boolean" label="convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" /> | |
| 235 <param name="cml_array" type="boolean" label="write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" /> | |
| 236 <param name="cml_aromatic" type="boolean" label="write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" /> | |
| 237 <param name="cml_hydrogen" type="boolean" label="use hydrogen Count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
| 238 <param name="cml_metadata" type="boolean" label="write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" /> | |
| 239 <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" /> | |
| 240 <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" /> | |
| 241 <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" /> | |
| 9 | 242 <param name="cml_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" /> |
| 243 <param name="cml_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> | |
| 7 | 244 </when> |
| 245 <when value="cmlr" /> | |
| 246 <when value="com" /> | |
| 247 <when value="copy" /> | |
| 248 <when value="crk2d" /> | |
| 249 <when value="crk3d" /> | |
| 250 <when value="csr" /> | |
| 251 <when value="cssr" /> | |
| 252 <when value="ct" /> | |
| 253 <when value="dmol" /> | |
| 254 <when value="fasta" /> | |
| 255 <when value="feat" /> | |
| 256 <when value="fh" /> | |
| 257 <when value="fix" /> | |
| 258 <when value="fpt"> | |
| 259 <param name="fpt_fptype" type="select" label="Fingerprint type"> | |
| 260 <option value="-xfFP2" selected="True">FP2</option> | |
| 261 <option value="-xfFP3">FP3</option> | |
| 262 <option value="-xfFP4">FP4</option> | |
| 263 <option value="-xfMACCS">MACCS</option> | |
| 264 </param> | |
| 265 <param name="fpt_fold" type="integer" value="0" size="20" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default"> | |
| 266 <validator type="in_range" min="0" /> | |
| 267 </param> | |
| 268 <param name="fpt_hex_multiple" type="boolean" label="hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
| 269 <param name="fpt_hex" type="boolean" label="hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" /> | |
| 270 <param name="fpt_set" type="boolean" label="describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" /> | |
| 271 <param name="fpt_unset" type="boolean" label="describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" /> | |
| 272 </when> | |
| 273 <when value="fract" /> | |
| 274 <when value="fs"> | |
| 275 <param name="fs_fptype" type="select" label="Fingerprint type"> | |
| 276 <option value="-xfFP2" selected="True">FP2</option> | |
| 277 <option value="-xfFP3">FP3</option> | |
| 278 <option value="-xfFP4">FP4</option> | |
| 279 <option value="-xfMACCS">MACCS</option> | |
| 280 </param> | |
| 281 <param name="fs_fold" type="integer" value="0" size="20" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default"> | |
| 282 <validator type="in_range" min="0" /> | |
| 283 </param> | |
| 284 </when> | |
| 285 <when value="gamin" /> | |
| 286 <when value="gau" /> | |
| 287 <when value="gpr" /> | |
| 288 <when value="gr96" /> | |
| 289 <when value="hin" /> | |
| 290 <when value="inchi"> | |
| 291 <param name="inchi_key" type="boolean" label="output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" /> | |
| 292 <param name="inchi_name" type="boolean" label="add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" /> | |
| 293 <param name="inchi_unique" type="boolean" label="output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" /> | |
| 294 <param name="inchi_unique_sort" type="boolean" label="output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" /> | |
| 295 <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="truncate InChI according to various parameters"> | |
| 296 <option value="/formula">formula only</option> | |
| 297 <option value="/connect">formula and connectivity only</option> | |
| 298 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> | |
| 299 <option value="/sp3">ignore sp3 stereochemistry</option> | |
| 300 <option value="/noEZ">ignore E/Z steroeochemistry</option> | |
| 301 <option value="/nochg">ignore charge and protonation</option> | |
| 302 <option value="/noiso">ignore isotopes</option> | |
| 303 </param> | |
| 304 | |
| 305 <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)."> | |
| 306 <option value="NEWPSOFF">Narrow End of Wedge Points to Stereo is OFF (NEWPSOFF - stdInChI)</option> | |
| 307 <option value="DoNotAddH">Skip the addition of hydrogen atoms (DoNotAddH - stdInChI)</option> | |
| 308 <option value="SNon">Exclude stereo (SNon - stdInChI)</option> | |
| 309 <option value="SRel">Relative stereo (SRel)</option> | |
| 310 <option value="SRac">Racemic stereo (SRac)</option> | |
| 311 <option value="SUCF">Use Chiral Flag (SUCF)</option> | |
| 312 <option value="ChiralFlagON">Set Chiral Flag (ChrialFlagON)</option> | |
| 313 <option value="ChiralFlagOFF">Set Not-Chiral Flag (ChrialFlagOFF)</option> | |
| 314 <option value="SUU">Include omitted unknown/undefined stereo (SUU)</option> | |
| 315 <option value="SLUUD">Stereo labels for "unknown" and "undefined" are different, 'u' and '?', respectively (SLUUD) </option> | |
| 316 <option value="FixedH">Mobile H Perception Off (FixedH)</option> | |
| 317 <option value="RecMet">Include reconnected bond to metal results (RecMet)</option> | |
| 318 <option value="KET">Keto-enol tautomerism (KET)</option> | |
| 319 <option value="15T">1,5-tautomerism (15T)</option> | |
| 320 </param> | |
| 321 </when> | |
| 322 <when value="inp" /> | |
| 323 <when value="jin" /> | |
| 324 <when value="mmd" /> | |
| 325 <when value="mmod" /> | |
| 326 <when value="mol2"> | |
| 327 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands (-xl)" truevalue="-xl" falsevalue="" checked="false" /> | |
| 9 | 328 <param name="mol2_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" /> |
| 329 <param name="mol2_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> | |
| 7 | 330 </when> |
| 331 <when value="molreport" /> | |
| 332 <when value="mop" /> | |
| 333 <when value="mopcrt" /> | |
| 334 <when value="mopin" /> | |
| 335 <when value="mpc" /> | |
| 336 <when value="mpd" /> | |
| 337 <when value="mpqcin" /> | |
| 338 <when value="nw" /> | |
| 339 <when value="pcm" /> | |
| 340 <when value="pdb" /> | |
| 341 <when value="pov" /> | |
| 342 <when value="pqs" /> | |
| 343 <when value="qcin" /> | |
| 344 <when value="report" /> | |
| 345 <when value="rxn" /> | |
| 346 <when value="sdf"> | |
| 347 <param name="sdf_exp_h" type="boolean" label="output V3000 not V2000 (used for >999 atoms/bonds) (-x3)" truevalue="-x3" falsevalue="" checked="false" /> | |
| 348 <param name="sdf_no_prop" type="boolean" label="write no properties (-xm)" truevalue="-xm" falsevalue="" checked="false" /> | |
| 349 <param name="sdf_wedge_bonds" type="boolean" label="use wedge and hash bonds from input (2D structures only) (-xw)" truevalue="-xw" falsevalue="" checked="false" /> | |
| 350 <param name="sdf_alias_out" type="boolean" label="output in Alias form, e.g. Ph (-xA)" truevalue="-xA" falsevalue="" checked="false" /> | |
| 9 | 351 <param name="sdf_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" /> |
| 352 <param name="sdf_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> | |
| 7 | 353 </when> |
| 354 <when value="smi"> | |
| 355 <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> | |
| 356 <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" /> | |
| 357 <param name="smi_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" /> | |
| 358 <param name="smi_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" /> | |
| 359 <param name="smi_can" type="boolean" label="Output in canonical form (-xc)" truevalue="-xc" falsevalue="" checked="false" /> | |
| 360 <param name="smi_coordinates" type="boolean" label="append X/Y coordinates in canonical-SMILES order (-xx)" truevalue="-xx" falsevalue="" checked="false" /> | |
| 361 </when> | |
| 362 <when value="tdd" /> | |
| 363 <when value="test" /> | |
| 364 <when value="therm" /> | |
| 365 <when value="tmol" /> | |
| 366 <when value="txyz" /> | |
| 367 <when value="unixyz" /> | |
| 368 <when value="vmol" /> | |
| 369 <when value="xed" /> | |
| 370 <when value="xyz" /> | |
| 371 <when value="yob" /> | |
| 372 <when value="zin" /> | |
| 373 </conditional> | |
| 374 | |
| 375 | |
| 376 <!-- Options for all formats.--> | |
| 377 <param name="remove_h" type="boolean" label="Delete hydrogen atoms, make all hydrogen implicit (-d)" truevalue="-d" falsevalue="" /> | |
| 378 <param name="ph" size="5" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/> | |
| 379 <param name="dative_bonds" type="boolean" label="Convert dative bonds, e.g. [N+]([O-])=O to N(=O)=O (-b)" truevalue="-b" falsevalue="" /> | |
| 380 | |
| 381 <param name="appendtotitle" type="text" value="" size="20" label="Append the specified text after each molecule title"/> | |
| 382 | |
| 383 <!-- Uniqueness --> | |
| 384 <conditional name="unique"> | |
| 385 <param name="unique_opts_selector" type="select" label="Uniqueness according to"> | |
| 386 <option value="" selected="True">No unique filter</option> | |
| 387 <option value="inchi">InChI</option> | |
| 388 <option value="cansmi">canonical SMILES with stereochemical information</option> | |
| 389 <option value="cansmiNS">canonical SMILES without stereochemical information</option> | |
| 390 <option value="title">title</option> | |
| 391 </param> | |
| 392 <when value="" /> | |
| 393 <when value="cansmi" /> | |
| 394 <when value="cansmiNS" /> | |
| 395 <when value="title" /> | |
| 396 <when value="inchi"> | |
| 397 <param name="truncate" type="select" multiple="True" display="checkboxes" label="Uniqueness defined as truncated InChI"> | |
| 398 <option value="/formula">formula only</option> | |
| 399 <option value="/connect">formula and connectivity only</option> | |
| 400 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> | |
| 401 <option value="/sp3">ignore sp3 stereochemistry</option> | |
| 402 <option value="/noEZ">ignore E/Z steroeochemistry</option> | |
| 403 <option value="/nochg">ignore charge and protonation</option> | |
| 404 <option value="/noiso">ignore isotopes</option> | |
| 405 </param> | |
| 406 </when> | |
| 407 </conditional> | |
| 0 | 408 </inputs> |
| 7 | 409 |
| 410 | |
| 0 | 411 <outputs> |
| 7 | 412 <data name="outfile" type="data" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}"> |
| 0 | 413 <change_format> |
| 7 | 414 <when input="oformat.oformat_opts_selector" value="sdf" format="sdf"/> |
| 415 <when input="oformat.oformat_opts_selector" value="can" format="smi"/> | |
| 416 <when input="oformat.oformat_opts_selector" value="smi" format="smi"/> | |
| 417 <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/> | |
| 418 <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/> | |
| 419 <when input="oformat.oformat_opts_selector" value="cml" format="cml"/> | |
| 420 <when input="oformat.oformat_opts_selector" value="mol" format="mol"/> | |
| 421 <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/> | |
| 422 <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/> | |
| 0 | 423 </change_format> |
| 424 </data> | |
| 425 </outputs> | |
| 426 <help> | |
| 427 | |
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428 .. class:: infomark |
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429 |
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430 **What this tool does** |
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431 |
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432 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. |
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433 The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) |
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434 others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). |
| 0 | 435 |
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436 ----- |
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437 |
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438 .. class:: infomark |
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439 |
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440 **Output** |
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441 |
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442 Can be specified manually. |
| 0 | 443 |
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444 ----- |
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445 |
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446 .. class:: infomark |
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447 |
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448 **Cite** |
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449 |
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450 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ |
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451 |
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452 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 |
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453 |
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454 `Open Babel`_ |
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455 |
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456 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page |
| 0 | 457 |
| 458 | |
| 459 </help> | |
| 460 </tool> |