Mercurial > repos > iuc > molecule_datatypes
view cml_to_smi_converter.xml @ 0:85eca06eefc6 draft default tip
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author | bgruening |
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date | Thu, 15 Aug 2013 03:19:26 -0400 |
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<tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0"> <description></description> <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism> <requirements> <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command > obabel -icml "${input}" #if $can: -ocan #else: -osmi #end if -O "${output}" -e $remove_h #if $iso_chi or $can or $exp_h: -x$iso_chi$exp_h$can #end if #if $dative_bonds: -b #end if #if int($ph) >= 0: -p $ph #end if 2>&1 </command> <inputs> <param name="input" type="data" format="cml" label="Molecules in CML-format"/> <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" /> <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" /> <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" /> <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" /> <param name="ph" size="3" 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="" /> </inputs> <outputs> <data name="output" format="smi"/> </outputs> <help> </help> </tool>