Mercurial > repos > bgruening > openbabel_compound_convert
diff ob_convert.xml @ 15:4242b4d68e9c 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 11:06:27 +0000 |
| parents | 1c66bf08f687 |
| children |
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--- a/ob_convert.xml Tue Nov 10 20:33:21 2020 +0000 +++ b/ob_convert.xml Thu Aug 15 11:06:27 2024 +0000 @@ -6,7 +6,7 @@ --> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"> @@ -132,7 +132,11 @@ #if float($ph) >= 0: -p $ph #end if - + + #if $appendproperties: + #set $props = str($appendproperties).replace(',', ' ') + --append '$props' + #end if ]]> </command> <inputs> @@ -155,7 +159,7 @@ <option value="cif">Crystallographic Information File</option> <option value="cml">Chemical Markup Language (CML)</option> <option value="cmlr">CML Reaction format</option> - <option value="com">Gaussian 98/03 Cartesian Input</option> + <option value="com">Gaussian 98/03 Cartesian Input(com)</option> <option value="copy">Copies raw text</option> <option value="crk2d">Chemical Resource Kit 2D diagram format</option> <option value="crk3d">Chemical Resource Kit 3D format</option> @@ -163,8 +167,6 @@ <option value="cssr">CSD CSSR format</option> <option value="ct">ChemDraw Connection Table format</option> <option value="dmol">DMol3 coordinates format</option> - <!--<option value="ent">Protein Data Bank format</option> - <option value="fa">FASTA format</option>--> <option value="fasta">FASTA format</option> <option value="feat">Feature format</option> <option value="fh">Fenske-Hall Z-Matrix format</option> @@ -172,27 +174,22 @@ <option value="fpt">Fingerprint format (fpt)</option> <option value="fract">Free Form Fractional format</option> <option value="fs">Open Babel FastSearching database (fs)</option> - <!--<option value="fsa">FASTA format</option>--> - <option value="gamin">GAMESS Input</option> - <option value="gau">Gaussian 98/03 Cartesian Input</option> - <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option> - <option value="gjf">Gaussian 98/03 Cartesian Input</option>--> + <option value="gamin">GAMESS Input (gamin)</option> + <option value="inp">GAMESS Input (inp)</option> + <option value="gau">Gaussian 98/03 Cartesian Input(gau)</option> <option value="gpr">Ghemical format</option> <option value="gr96">GROMOS96 format</option> <option value="hin">HyperChem HIN format</option> <option value="inchi">IUPAC InChI</option> - <option value="inp">GAMESS Input</option> <option value="jin">Jaguar input format</option> - <!--<option value="mdl">MDL MOL format (mol)</option>--> - <option value="mmd">MacroModel format</option> - <option value="mmod">MacroModel format</option> - <!--<option value="mol">MDL MOL format (mol)</option> use SDF--> + <option value="mmd">MacroModel format (mmd)</option> + <option value="mmod">MacroModel format (mmod)</option> <option value="mol2">Sybyl Mol2 format (mol2)</option> <option value="molreport">Open Babel molecule report</option> - <option value="mop">MOPAC Cartesian format</option> - <option value="mopcrt">MOPAC Cartesian format</option> + <option value="mop">MOPAC Cartesian format (mop)</option> + <option value="mopcrt">MOPAC Cartesian format (mopcrt)</option> <option value="mopin">MOPAC Internal</option> - <option value="mpc">MOPAC Cartesian format</option> + <option value="mpc">MOPAC Cartesian format (mpc)</option> <option value="mpd">Sybyl descriptor format</option> <option value="mpqcin">MPQC simplified input format</option> <option value="nw">NWChem input format</option> @@ -204,13 +201,11 @@ <option value="qcin">Q-Chem input format</option> <option value="report">Open Babel report format</option> <option value="rxn">MDL RXN format</option> - <!--<option value="sd">MDL MOL format</option>--> <option value="sdf">MDL MOL format (sdf, mol)</option> <option value="smi">SMILES format (smi)</option> - <!--<option value="sy2">Sybyl Mol2 format</option>--> - <option value="tdd">Thermo format</option> + <option value="tdd">Thermo format (tdd)</option> <option value="test">Test format</option> - <option value="therm">Thermo format</option> + <option value="therm">Thermo format (therm)</option> <option value="tmol">TurboMole Coordinate format</option> <option value="txyz">Tinker MM2 format</option> <option value="unixyz">UniChem XYZ format</option> @@ -398,6 +393,27 @@ <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue="" label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" /> <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/> + <param name="appendproperties" type="select" multiple="true" label="Molecular properties to append to the title." optional="true"> + <option value="abonds">Number of aromatic bonds</option> + <option value="atoms">Number of atoms</option> + <option value="bonds">Number of bonds</option> + <option value="cansmi">Canonical SMILES</option> + <option value="cansmiNS">Canonical SMILES without isotopes or stereo</option> + <option value="dbonds">Number of double bonds</option> + <option value="sbonds">Number of single bonds</option> + <option value="tbonds">Number of triple bonds</option> + <option value="formula">Chemical formula</option> + <option value="HBA1">Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> + <option value="HBA2">Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> + <option value="HBD">Number of Hydrogen Bond Donors (JoelLib)</option> + <option value="InChI">IUPAC InChI identifier</option> + <option value="InChIKey">InChIKey</option> + <option value="L5">Lipinski Rule of Five</option> + <option value="logP">octanol/water partition coefficient</option> + <option value="MR">molar refractivity</option> + <option value="MW">Molecular Weight</option> + <option value="TPSA">topological polar surface area</option> + </param> <!-- Uniqueness --> <conditional name="unique"> @@ -449,40 +465,40 @@ </collection> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat_opts_selector" value="cml" /> <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" /> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat_opts_selector" value="fs" /> - <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs"> + <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs" > <extra_files type="file" value="molecule.sdf" name="molecule.sdf" /> <extra_files type="file" value="molecule.fs" name="molecule.fs" compare="sim_size" /> </output> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat_opts_selector" value="inchi" /> <output name="outfile" ftype="inchi" file="ob_convert_on_CID2244.inchi" /> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat_opts_selector" value="pdb" /> <output name="outfile" ftype="pdb" file="ob_convert_on_CID2244.pdb" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat_opts_selector" value="can" /> <output name="outfile" ftype="smi" file="ob_convert_on_CID2244.smi" /> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat_opts_selector" value="sdf" /> <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" ftype="smi" value="2_mol.smi"/> <param name="oformat_opts_selector" value="pdbqt"/> <param name="split" value="true"/> @@ -491,6 +507,12 @@ <element name="molecule2" file="split2.pdbqt" /> </output_collection> </test> + <test expect_num_outputs="1"> + <param name="infile" ftype="smi" value="2_mol.smi"/> + <param name="oformat_opts_selector" value="sdf" /> + <param name="appendproperties" value="cansmi,InChI"/> + <output name="outfile" ftype="sdf" file="2_mol.sdf" lines_diff="4"/> + </test> </tests> <help> <![CDATA[