Mercurial > repos > bgruening > openbabel_compound_convert
comparison ob_convert.xml @ 16:b1dda415eecd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2024 10:59:50 +0000 |
| parents | db1d1e4658ea |
| children |
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| 15:1ca45f402ce8 | 16:b1dda415eecd |
|---|---|
| 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> |
| 8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
| 9 <token name="@GALAXY_VERSION@">0</token> | 9 <token name="@GALAXY_VERSION@">1</token> |
| 10 </macros> | 10 </macros> |
| 11 <expand macro="requirements"/> | 11 <expand macro="requirements"/> |
| 12 <command detect_errors="aggressive"> | 12 <command detect_errors="aggressive"> |
| 13 <![CDATA[ | 13 <![CDATA[ |
| 14 | 14 |
| 130 $dative_bonds | 130 $dative_bonds |
| 131 | 131 |
| 132 #if float($ph) >= 0: | 132 #if float($ph) >= 0: |
| 133 -p $ph | 133 -p $ph |
| 134 #end if | 134 #end if |
| 135 | 135 |
| 136 #if $appendproperties: | |
| 137 #set $props = str($appendproperties).replace(',', ' ') | |
| 138 --append '$props' | |
| 139 #end if | |
| 136 ]]> | 140 ]]> |
| 137 </command> | 141 </command> |
| 138 <inputs> | 142 <inputs> |
| 139 <expand macro="infile_all_types"/> | 143 <expand macro="infile_all_types"/> |
| 140 <conditional name="oformat"> | 144 <conditional name="oformat"> |
| 153 <option value="cdxml">ChemDraw CDXML format</option> | 157 <option value="cdxml">ChemDraw CDXML format</option> |
| 154 <option value="cht">Chemtool format</option> | 158 <option value="cht">Chemtool format</option> |
| 155 <option value="cif">Crystallographic Information File</option> | 159 <option value="cif">Crystallographic Information File</option> |
| 156 <option value="cml">Chemical Markup Language (CML)</option> | 160 <option value="cml">Chemical Markup Language (CML)</option> |
| 157 <option value="cmlr">CML Reaction format</option> | 161 <option value="cmlr">CML Reaction format</option> |
| 158 <option value="com">Gaussian 98/03 Cartesian Input</option> | 162 <option value="com">Gaussian 98/03 Cartesian Input(com)</option> |
| 159 <option value="copy">Copies raw text</option> | 163 <option value="copy">Copies raw text</option> |
| 160 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> | 164 <option value="crk2d">Chemical Resource Kit 2D diagram format</option> |
| 161 <option value="crk3d">Chemical Resource Kit 3D format</option> | 165 <option value="crk3d">Chemical Resource Kit 3D format</option> |
| 162 <option value="csr">Accelrys/MSI Quanta CSR format</option> | 166 <option value="csr">Accelrys/MSI Quanta CSR format</option> |
| 163 <option value="cssr">CSD CSSR format</option> | 167 <option value="cssr">CSD CSSR format</option> |
| 164 <option value="ct">ChemDraw Connection Table format</option> | 168 <option value="ct">ChemDraw Connection Table format</option> |
| 165 <option value="dmol">DMol3 coordinates format</option> | 169 <option value="dmol">DMol3 coordinates format</option> |
| 166 <!--<option value="ent">Protein Data Bank format</option> | |
| 167 <option value="fa">FASTA format</option>--> | |
| 168 <option value="fasta">FASTA format</option> | 170 <option value="fasta">FASTA format</option> |
| 169 <option value="feat">Feature format</option> | 171 <option value="feat">Feature format</option> |
| 170 <option value="fh">Fenske-Hall Z-Matrix format</option> | 172 <option value="fh">Fenske-Hall Z-Matrix format</option> |
| 171 <option value="fix">SMILES FIX format</option> | 173 <option value="fix">SMILES FIX format</option> |
| 172 <option value="fpt">Fingerprint format (fpt)</option> | 174 <option value="fpt">Fingerprint format (fpt)</option> |
| 173 <option value="fract">Free Form Fractional format</option> | 175 <option value="fract">Free Form Fractional format</option> |
| 174 <option value="fs">Open Babel FastSearching database (fs)</option> | 176 <option value="fs">Open Babel FastSearching database (fs)</option> |
| 175 <!--<option value="fsa">FASTA format</option>--> | 177 <option value="gamin">GAMESS Input (gamin)</option> |
| 176 <option value="gamin">GAMESS Input</option> | 178 <option value="inp">GAMESS Input (inp)</option> |
| 177 <option value="gau">Gaussian 98/03 Cartesian Input</option> | 179 <option value="gau">Gaussian 98/03 Cartesian Input(gau)</option> |
| 178 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option> | |
| 179 <option value="gjf">Gaussian 98/03 Cartesian Input</option>--> | |
| 180 <option value="gpr">Ghemical format</option> | 180 <option value="gpr">Ghemical format</option> |
| 181 <option value="gr96">GROMOS96 format</option> | 181 <option value="gr96">GROMOS96 format</option> |
| 182 <option value="hin">HyperChem HIN format</option> | 182 <option value="hin">HyperChem HIN format</option> |
| 183 <option value="inchi">IUPAC InChI</option> | 183 <option value="inchi">IUPAC InChI</option> |
| 184 <option value="inp">GAMESS Input</option> | |
| 185 <option value="jin">Jaguar input format</option> | 184 <option value="jin">Jaguar input format</option> |
| 186 <!--<option value="mdl">MDL MOL format (mol)</option>--> | 185 <option value="mmd">MacroModel format (mmd)</option> |
| 187 <option value="mmd">MacroModel format</option> | 186 <option value="mmod">MacroModel format (mmod)</option> |
| 188 <option value="mmod">MacroModel format</option> | |
| 189 <!--<option value="mol">MDL MOL format (mol)</option> use SDF--> | |
| 190 <option value="mol2">Sybyl Mol2 format (mol2)</option> | 187 <option value="mol2">Sybyl Mol2 format (mol2)</option> |
| 191 <option value="molreport">Open Babel molecule report</option> | 188 <option value="molreport">Open Babel molecule report</option> |
| 192 <option value="mop">MOPAC Cartesian format</option> | 189 <option value="mop">MOPAC Cartesian format (mop)</option> |
| 193 <option value="mopcrt">MOPAC Cartesian format</option> | 190 <option value="mopcrt">MOPAC Cartesian format (mopcrt)</option> |
| 194 <option value="mopin">MOPAC Internal</option> | 191 <option value="mopin">MOPAC Internal</option> |
| 195 <option value="mpc">MOPAC Cartesian format</option> | 192 <option value="mpc">MOPAC Cartesian format (mpc)</option> |
| 196 <option value="mpd">Sybyl descriptor format</option> | 193 <option value="mpd">Sybyl descriptor format</option> |
| 197 <option value="mpqcin">MPQC simplified input format</option> | 194 <option value="mpqcin">MPQC simplified input format</option> |
| 198 <option value="nw">NWChem input format</option> | 195 <option value="nw">NWChem input format</option> |
| 199 <option value="pcm">PCModel format</option> | 196 <option value="pcm">PCModel format</option> |
| 200 <option value="pdb">Protein Data Bank format (pdb)</option> | 197 <option value="pdb">Protein Data Bank format (pdb)</option> |
| 202 <option value="pov">POV-Ray input format</option> | 199 <option value="pov">POV-Ray input format</option> |
| 203 <option value="pqs">Parallel Quantum Solutions format</option> | 200 <option value="pqs">Parallel Quantum Solutions format</option> |
| 204 <option value="qcin">Q-Chem input format</option> | 201 <option value="qcin">Q-Chem input format</option> |
| 205 <option value="report">Open Babel report format</option> | 202 <option value="report">Open Babel report format</option> |
| 206 <option value="rxn">MDL RXN format</option> | 203 <option value="rxn">MDL RXN format</option> |
| 207 <!--<option value="sd">MDL MOL format</option>--> | |
| 208 <option value="sdf">MDL MOL format (sdf, mol)</option> | 204 <option value="sdf">MDL MOL format (sdf, mol)</option> |
| 209 <option value="smi">SMILES format (smi)</option> | 205 <option value="smi">SMILES format (smi)</option> |
| 210 <!--<option value="sy2">Sybyl Mol2 format</option>--> | 206 <option value="tdd">Thermo format (tdd)</option> |
| 211 <option value="tdd">Thermo format</option> | |
| 212 <option value="test">Test format</option> | 207 <option value="test">Test format</option> |
| 213 <option value="therm">Thermo format</option> | 208 <option value="therm">Thermo format (therm)</option> |
| 214 <option value="tmol">TurboMole Coordinate format</option> | 209 <option value="tmol">TurboMole Coordinate format</option> |
| 215 <option value="txyz">Tinker MM2 format</option> | 210 <option value="txyz">Tinker MM2 format</option> |
| 216 <option value="unixyz">UniChem XYZ format</option> | 211 <option value="unixyz">UniChem XYZ format</option> |
| 217 <option value="vmol">ViewMol format</option> | 212 <option value="vmol">ViewMol format</option> |
| 218 <option value="xed">XED format</option> | 213 <option value="xed">XED format</option> |
| 396 label="Delete hydrogen atoms, make all hydrogens implicit" help="(-d)" /> | 391 label="Delete hydrogen atoms, make all hydrogens implicit" help="(-d)" /> |
| 397 <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/> | 392 <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/> |
| 398 <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue="" | 393 <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue="" |
| 399 label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" /> | 394 label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" /> |
| 400 <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/> | 395 <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/> |
| 396 <param name="appendproperties" type="select" multiple="true" label="Molecular properties to append to the title." optional="true"> | |
| 397 <option value="abonds">Number of aromatic bonds</option> | |
| 398 <option value="atoms">Number of atoms</option> | |
| 399 <option value="bonds">Number of bonds</option> | |
| 400 <option value="cansmi">Canonical SMILES</option> | |
| 401 <option value="cansmiNS">Canonical SMILES without isotopes or stereo</option> | |
| 402 <option value="dbonds">Number of double bonds</option> | |
| 403 <option value="sbonds">Number of single bonds</option> | |
| 404 <option value="tbonds">Number of triple bonds</option> | |
| 405 <option value="formula">Chemical formula</option> | |
| 406 <option value="HBA1">Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> | |
| 407 <option value="HBA2">Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> | |
| 408 <option value="HBD">Number of Hydrogen Bond Donors (JoelLib)</option> | |
| 409 <option value="InChI">IUPAC InChI identifier</option> | |
| 410 <option value="InChIKey">InChIKey</option> | |
| 411 <option value="L5">Lipinski Rule of Five</option> | |
| 412 <option value="logP">octanol/water partition coefficient</option> | |
| 413 <option value="MR">molar refractivity</option> | |
| 414 <option value="MW">Molecular Weight</option> | |
| 415 <option value="TPSA">topological polar surface area</option> | |
| 416 </param> | |
| 401 | 417 |
| 402 <!-- Uniqueness --> | 418 <!-- Uniqueness --> |
| 403 <conditional name="unique"> | 419 <conditional name="unique"> |
| 404 <param name="unique_opts_selector" type="select" label="Uniqueness according to"> | 420 <param name="unique_opts_selector" type="select" label="Uniqueness according to"> |
| 405 <option value="" selected="True">No unique filter</option> | 421 <option value="" selected="True">No unique filter</option> |
| 447 <filter>split == True</filter> | 463 <filter>split == True</filter> |
| 448 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" /> | 464 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" /> |
| 449 </collection> | 465 </collection> |
| 450 </outputs> | 466 </outputs> |
| 451 <tests> | 467 <tests> |
| 452 <test> | 468 <test expect_num_outputs="1"> |
| 453 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | 469 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
| 454 <param name="oformat_opts_selector" value="cml" /> | 470 <param name="oformat_opts_selector" value="cml" /> |
| 455 <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" /> | 471 <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" /> |
| 456 </test> | 472 </test> |
| 457 <test> | 473 <test expect_num_outputs="1"> |
| 458 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | 474 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
| 459 <param name="oformat_opts_selector" value="fs" /> | 475 <param name="oformat_opts_selector" value="fs" /> |
| 460 <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs"> | 476 <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs" > |
| 461 <extra_files type="file" value="molecule.sdf" name="molecule.sdf" /> | 477 <extra_files type="file" value="molecule.sdf" name="molecule.sdf" /> |
| 462 <extra_files type="file" value="molecule.fs" name="molecule.fs" compare="sim_size" /> | 478 <extra_files type="file" value="molecule.fs" name="molecule.fs" compare="sim_size" /> |
| 463 </output> | 479 </output> |
| 464 </test> | 480 </test> |
| 465 <test> | 481 <test expect_num_outputs="1"> |
| 466 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | 482 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
| 467 <param name="oformat_opts_selector" value="inchi" /> | 483 <param name="oformat_opts_selector" value="inchi" /> |
| 468 <output name="outfile" ftype="inchi" file="ob_convert_on_CID2244.inchi" /> | 484 <output name="outfile" ftype="inchi" file="ob_convert_on_CID2244.inchi" /> |
| 469 </test> | 485 </test> |
| 470 <test> | 486 <test expect_num_outputs="1"> |
| 471 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | 487 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
| 472 <param name="oformat_opts_selector" value="pdb" /> | 488 <param name="oformat_opts_selector" value="pdb" /> |
| 473 <output name="outfile" ftype="pdb" file="ob_convert_on_CID2244.pdb" lines_diff="4" /> | 489 <output name="outfile" ftype="pdb" file="ob_convert_on_CID2244.pdb" lines_diff="4" /> |
| 474 </test> | 490 </test> |
| 475 <test> | 491 <test expect_num_outputs="1"> |
| 476 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | 492 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
| 477 <param name="oformat_opts_selector" value="can" /> | 493 <param name="oformat_opts_selector" value="can" /> |
| 478 <output name="outfile" ftype="smi" file="ob_convert_on_CID2244.smi" /> | 494 <output name="outfile" ftype="smi" file="ob_convert_on_CID2244.smi" /> |
| 479 </test> | 495 </test> |
| 480 <test> | 496 <test expect_num_outputs="1"> |
| 481 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> | 497 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
| 482 <param name="oformat_opts_selector" value="sdf" /> | 498 <param name="oformat_opts_selector" value="sdf" /> |
| 483 <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/> | 499 <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/> |
| 484 </test> | 500 </test> |
| 485 <test> | 501 <test expect_num_outputs="1"> |
| 486 <param name="infile" ftype="smi" value="2_mol.smi"/> | 502 <param name="infile" ftype="smi" value="2_mol.smi"/> |
| 487 <param name="oformat_opts_selector" value="pdbqt"/> | 503 <param name="oformat_opts_selector" value="pdbqt"/> |
| 488 <param name="split" value="true"/> | 504 <param name="split" value="true"/> |
| 489 <output_collection name="file_outputs" type="list" count="2"> | 505 <output_collection name="file_outputs" type="list" count="2"> |
| 490 <element name="molecule1" file="split1.pdbqt" /> | 506 <element name="molecule1" file="split1.pdbqt" /> |
| 491 <element name="molecule2" file="split2.pdbqt" /> | 507 <element name="molecule2" file="split2.pdbqt" /> |
| 492 </output_collection> | 508 </output_collection> |
| 493 </test> | 509 </test> |
| 510 <test expect_num_outputs="1"> | |
| 511 <param name="infile" ftype="smi" value="2_mol.smi"/> | |
| 512 <param name="oformat_opts_selector" value="sdf" /> | |
| 513 <param name="appendproperties" value="cansmi,InChI"/> | |
| 514 <output name="outfile" ftype="sdf" file="2_mol.sdf" lines_diff="4"/> | |
| 515 </test> | |
| 494 </tests> | 516 </tests> |
| 495 <help> | 517 <help> |
| 496 <![CDATA[ | 518 <![CDATA[ |
| 497 | 519 |
| 498 .. class:: infomark | 520 .. class:: infomark |