Mercurial > repos > bgruening > openbabel
diff convert/ob_convert.xml @ 0:527ecd2fc500 draft
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| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2013 03:25:06 -0400 |
| parents | |
| children | 125da3a296ca |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert/ob_convert.xml Thu Aug 15 03:25:06 2013 -0400 @@ -0,0 +1,460 @@ +<tool id="ctb_compound_convert" name="Compound Convert" version="0.1"> + <description>Converts various chemistry and molecular modeling data files</description> + <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> + 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 + and run the job in non-multi mode. + --> + <requirements> + <requirement type="package" version="2.3.2">openbabel</requirement> + </requirements> + <command> +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces + +#set $format = $oformat.oformat_opts_selector + + #if $format == "fs": + ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs. + ## Because openbabel likes file extensions, we give the molecule file a proper file extension. + mkdir $outfile.extra_files_path; + cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}; + #end if + +obabel -i "${infile.ext}" + + #if $format == "fs": + ## the fs filetype need his own symlink path, all others can take the original ones + ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )} + -o "$format" -e + -O ${os.path.join($outfile.extra_files_path,'molecule.fs')} + #if int($oformat.fs_fold) > 0: + -xN$oformat.fs_fold + #end if + ${oformat.fs_fptype} + #else: + "${infile}" + -o "$format" + -O "${outfile}" + -e + #end if + + + #if $format == 'cml': + $oformat.cml_array + $oformat.cml_cml1 + $oformat.cml_aromatic + $oformat.cml_hydrogen + $oformat.cml_metadata + $oformat.cml_omit + $oformat.cml_continuous + $oformat.cml_properties + $oformat.cml_gen2d + $oformat.cml_gen3d + #elif $format == 'inchi': + ##ignore less import warnings + -w + #if $oformat.inchi_truncate: + #set $truncate = ''.join( str( $oformat.inchi_truncate ).split( ',' ) ) + -xT ${truncate} + #end if + + #if $oformat.inchi_additional: + #set $additional = ' '.join( str( $oformat.inchi_additional ).split( ',' ) ) + -xX '${additional}' + #end if + + $oformat.inchi_key + $oformat.inchi_name + $oformat.inchi_unique + $oformat.inchi_unique_sort + #elif $format == 'can': + $oformat.can_exp_h + $oformat.can_iso_chi + $oformat.can_rad + $oformat.can_atomclass_out + #elif $format == 'smi': + $oformat.smi_exp_h + $oformat.smi_iso_chi + $oformat.smi_rad + $oformat.smi_atomclass_out + $oformat.smi_can + $oformat.smi_coordinates + #elif $format == 'sdf': + $oformat.sdf_exp_h + $oformat.sdf_no_prop + $oformat.sdf_wedge_bonds + $oformat.sdf_alias_out + $oformat.sdf_gen2d + $oformat.sdf_gen3d + #elif $format == 'fpt': + $oformat.fpt_fptype + #if int($oformat.fpt_fold) > 0: + $oformat.fpt_fold + #end if + $oformat.fpt_hex_multiple + $oformat.fpt_hex + $oformat.fpt_set + $oformat.fpt_unset + #elif $format == 'mol2': + $oformat.mol2_ignore_res + $oformat.mol2_gen2d + $oformat.mol2_gen3d + #end if + + ## Uniqueness according to stripped InChI's or canonical SMILES + #if str($unique.unique_opts_selector): + #if $unique.unique_opts_selector == 'inchi': + #if $unique.truncate: + #set $truncate = ''.join( str( $unique.truncate ).split( ',' ) ) + --unique $truncate + #end if + #else + --unique $unique.unique_opts_selector + #end if + #end if + + + #if str($appendtotitle).strip(): + --addtotitle '${appendtotitle}' + #end if + + $remove_h + $dative_bonds + + #if int($ph) >= 0: + -p $ph + #end if + + 2>&1 + </command> + <inputs> + <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/> + <conditional name="oformat"> + <param name="oformat_opts_selector" type="select" label="Output format"> + <option value="acr">Carine ASCI Crystal</option> + <option value="alc">Alchemy format</option> + <option value="bgf">MSI BGF format</option> + <option value="box">Dock 3.5 Box format</option> + <option value="bs">Ball and Stick format</option> + <option value="c3d1">Chem3D Cartesian 1 format</option> + <option value="c3d2">Chem3D Cartesian 2 format</option> + <option value="caccrt">Cacao Cartesian format</option> + <option value="cache">CAChe MolStruct format</option> + <option value="cacint">Cacao Internal format</option> + <option value="can" selected="True">Canonical SMILES format (can)</option> + <option value="cdxml">ChemDraw CDXML format</option> + <option value="cht">Chemtool format</option> + <option value="cif">Crystallographic Information File</option> + <option value="cml">Chemical Markup Language</option> + <option value="cmlr">CML Reaction format</option> + <option value="com">Gaussian 98/03 Cartesian Input</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> + <option value="csr">Accelrys/MSI Quanta CSR format</option> + <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> + <option value="fix">SMILES FIX format</option> + <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="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="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="mopin">MOPAC Internal</option> + <option value="mpc">MOPAC Cartesian format</option> + <option value="mpd">Sybyl descriptor format</option> + <option value="mpqcin">MPQC simplified input format</option> + <option value="nw">NWChem input format</option> + <option value="pcm">PCModel format</option> + <option value="pdb">Protein Data Bank format (pdb)</option> + <option value="pov">POV-Ray input format</option> + <option value="pqs">Parallel Quantum Solutions format</option> + <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="test">Test format</option> + <option value="therm">Thermo format</option> + <option value="tmol">TurboMole Coordinate format</option> + <option value="txyz">Tinker MM2 format</option> + <option value="unixyz">UniChem XYZ format</option> + <option value="vmol">ViewMol format</option> + <option value="xed">XED format</option> + <option value="xyz">XYZ cartesian coordinates format</option> + <option value="yob">YASARA.org YOB format</option> + <option value="zin">ZINDO input format</option> + </param> + <when value="acr" /> + <when value="alc" /> + <when value="bgf" /> + <when value="box" /> + <when value="bs" /> + <when value="c3d1" /> + <when value="c3d2" /> + <when value="caccrt" /> + <when value="cache" /> + <when value="cacint" /> + <when value="can"> + <param name="can_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="can_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" /> + <param name="can_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" /> + <param name="can_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" /> + </when> + <when value="cdxml" /> + <when value="cht" /> + <when value="cif" /> + <when value="cml"> + <param name="cml_cml1" type="boolean" label="convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" /> + <param name="cml_array" type="boolean" label="write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" /> + <param name="cml_aromatic" type="boolean" label="write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" /> + <param name="cml_hydrogen" type="boolean" label="use hydrogen Count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="cml_metadata" type="boolean" label="write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" /> + <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" /> + <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" /> + <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" /> + <param name="cml_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" /> + <param name="cml_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> + </when> + <when value="cmlr" /> + <when value="com" /> + <when value="copy" /> + <when value="crk2d" /> + <when value="crk3d" /> + <when value="csr" /> + <when value="cssr" /> + <when value="ct" /> + <when value="dmol" /> + <when value="fasta" /> + <when value="feat" /> + <when value="fh" /> + <when value="fix" /> + <when value="fpt"> + <param name="fpt_fptype" type="select" label="Fingerprint type"> + <option value="-xfFP2" selected="True">FP2</option> + <option value="-xfFP3">FP3</option> + <option value="-xfFP4">FP4</option> + <option value="-xfMACCS">MACCS</option> + </param> + <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"> + <validator type="in_range" min="0" /> + </param> + <param name="fpt_hex_multiple" type="boolean" label="hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="fpt_hex" type="boolean" label="hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" /> + <param name="fpt_set" type="boolean" label="describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" /> + <param name="fpt_unset" type="boolean" label="describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" /> + </when> + <when value="fract" /> + <when value="fs"> + <param name="fs_fptype" type="select" label="Fingerprint type"> + <option value="-xfFP2" selected="True">FP2</option> + <option value="-xfFP3">FP3</option> + <option value="-xfFP4">FP4</option> + <option value="-xfMACCS">MACCS</option> + </param> + <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"> + <validator type="in_range" min="0" /> + </param> + </when> + <when value="gamin" /> + <when value="gau" /> + <when value="gpr" /> + <when value="gr96" /> + <when value="hin" /> + <when value="inchi"> + <param name="inchi_key" type="boolean" label="output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" /> + <param name="inchi_name" type="boolean" label="add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" /> + <param name="inchi_unique" type="boolean" label="output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" /> + <param name="inchi_unique_sort" type="boolean" label="output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" /> + <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="truncate InChI according to various parameters"> + <option value="/formula">formula only</option> + <option value="/connect">formula and connectivity only</option> + <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> + <option value="/sp3">ignore sp3 stereochemistry</option> + <option value="/noEZ">ignore E/Z steroeochemistry</option> + <option value="/nochg">ignore charge and protonation</option> + <option value="/noiso">ignore isotopes</option> + </param> + + <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)."> + <option value="NEWPSOFF">Narrow End of Wedge Points to Stereo is OFF (NEWPSOFF - stdInChI)</option> + <option value="DoNotAddH">Skip the addition of hydrogen atoms (DoNotAddH - stdInChI)</option> + <option value="SNon">Exclude stereo (SNon - stdInChI)</option> + <option value="SRel">Relative stereo (SRel)</option> + <option value="SRac">Racemic stereo (SRac)</option> + <option value="SUCF">Use Chiral Flag (SUCF)</option> + <option value="ChiralFlagON">Set Chiral Flag (ChrialFlagON)</option> + <option value="ChiralFlagOFF">Set Not-Chiral Flag (ChrialFlagOFF)</option> + <option value="SUU">Include omitted unknown/undefined stereo (SUU)</option> + <option value="SLUUD">Stereo labels for "unknown" and "undefined" are different, 'u' and '?', respectively (SLUUD) </option> + <option value="FixedH">Mobile H Perception Off (FixedH)</option> + <option value="RecMet">Include reconnected bond to metal results (RecMet)</option> + <option value="KET">Keto-enol tautomerism (KET)</option> + <option value="15T">1,5-tautomerism (15T)</option> + </param> + </when> + <when value="inp" /> + <when value="jin" /> + <when value="mmd" /> + <when value="mmod" /> + <when value="mol2"> + <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands (-xl)" truevalue="-xl" falsevalue="" checked="false" /> + <param name="mol2_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" /> + <param name="mol2_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> + </when> + <when value="molreport" /> + <when value="mop" /> + <when value="mopcrt" /> + <when value="mopin" /> + <when value="mpc" /> + <when value="mpd" /> + <when value="mpqcin" /> + <when value="nw" /> + <when value="pcm" /> + <when value="pdb" /> + <when value="pov" /> + <when value="pqs" /> + <when value="qcin" /> + <when value="report" /> + <when value="rxn" /> + <when value="sdf"> + <param name="sdf_exp_h" type="boolean" label="output V3000 not V2000 (used for >999 atoms/bonds) (-x3)" truevalue="-x3" falsevalue="" checked="false" /> + <param name="sdf_no_prop" type="boolean" label="write no properties (-xm)" truevalue="-xm" falsevalue="" checked="false" /> + <param name="sdf_wedge_bonds" type="boolean" label="use wedge and hash bonds from input (2D structures only) (-xw)" truevalue="-xw" falsevalue="" checked="false" /> + <param name="sdf_alias_out" type="boolean" label="output in Alias form, e.g. Ph (-xA)" truevalue="-xA" falsevalue="" checked="false" /> + <param name="sdf_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" /> + <param name="sdf_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> + </when> + <when value="smi"> + <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" /> + <param name="smi_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" /> + <param name="smi_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" /> + <param name="smi_can" type="boolean" label="Output in canonical form (-xc)" truevalue="-xc" falsevalue="" checked="false" /> + <param name="smi_coordinates" type="boolean" label="append X/Y coordinates in canonical-SMILES order (-xx)" truevalue="-xx" falsevalue="" checked="false" /> + </when> + <when value="tdd" /> + <when value="test" /> + <when value="therm" /> + <when value="tmol" /> + <when value="txyz" /> + <when value="unixyz" /> + <when value="vmol" /> + <when value="xed" /> + <when value="xyz" /> + <when value="yob" /> + <when value="zin" /> + </conditional> + + + <!-- Options for all formats.--> + <param name="remove_h" type="boolean" label="Delete hydrogen atoms, make all hydrogen implicit (-d)" truevalue="-d" falsevalue="" /> + <param name="ph" size="5" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/> + <param name="dative_bonds" type="boolean" label="Convert dative bonds, e.g. [N+]([O-])=O to N(=O)=O (-b)" truevalue="-b" falsevalue="" /> + + <param name="appendtotitle" type="text" value="" size="20" label="Append the specified text after each molecule title"/> + + <!-- Uniqueness --> + <conditional name="unique"> + <param name="unique_opts_selector" type="select" label="Uniqueness according to"> + <option value="" selected="True">No unique filter</option> + <option value="inchi">InChI</option> + <option value="cansmi">canonical SMILES with stereochemical information</option> + <option value="cansmiNS">canonical SMILES without stereochemical information</option> + <option value="title">title</option> + </param> + <when value="" /> + <when value="cansmi" /> + <when value="cansmiNS" /> + <when value="title" /> + <when value="inchi"> + <param name="truncate" type="select" multiple="True" display="checkboxes" label="Uniqueness defined as truncated InChI"> + <option value="/formula">formula only</option> + <option value="/connect">formula and connectivity only</option> + <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> + <option value="/sp3">ignore sp3 stereochemistry</option> + <option value="/noEZ">ignore E/Z steroeochemistry</option> + <option value="/nochg">ignore charge and protonation</option> + <option value="/noiso">ignore isotopes</option> + </param> + </when> + </conditional> + </inputs> + + + <outputs> + <data name="outfile" type="data" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}"> + <change_format> + <when input="oformat.oformat_opts_selector" value="sdf" format="sdf"/> + <when input="oformat.oformat_opts_selector" value="can" format="smi"/> + <when input="oformat.oformat_opts_selector" value="smi" format="smi"/> + <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/> + <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/> + <when input="oformat.oformat_opts_selector" value="cml" format="cml"/> + <when input="oformat.oformat_opts_selector" value="mol" format="mol"/> + <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/> + <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/> + </change_format> + </data> + </outputs> + <help> + +.. class:: infomark + +**What this tool does** + +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. +The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) +others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). + +----- + +.. class:: infomark + +**Output** + +Can be specified manually. + +----- + +.. class:: infomark + +**Cite** + +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page + + + </help> +</tool>