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comparison ob_convert.xml @ 15:4242b4d68e9c draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:06:27 +0000
parents 1c66bf08f687
children
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14:e2c36f62e22f 15:4242b4d68e9c
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