Mercurial > repos > iuc > molecule_datatypes
comparison cml_to_smi_converter.xml @ 0:85eca06eefc6 draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2013 03:19:26 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:85eca06eefc6 |
|---|---|
| 1 <tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0"> | |
| 2 <description></description> | |
| 3 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.3.2">openbabel</requirement> | |
| 6 </requirements> | |
| 7 <command > | |
| 8 obabel -icml "${input}" | |
| 9 #if $can: | |
| 10 -ocan | |
| 11 #else: | |
| 12 -osmi | |
| 13 #end if | |
| 14 -O "${output}" -e | |
| 15 $remove_h | |
| 16 #if $iso_chi or $can or $exp_h: | |
| 17 -x$iso_chi$exp_h$can | |
| 18 #end if | |
| 19 #if $dative_bonds: | |
| 20 -b | |
| 21 #end if | |
| 22 #if int($ph) >= 0: | |
| 23 -p $ph | |
| 24 #end if | |
| 25 | |
| 26 2>&1 | |
| 27 </command> | |
| 28 <inputs> | |
| 29 <param name="input" type="data" format="cml" label="Molecules in CML-format"/> | |
| 30 <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" /> | |
| 31 <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" /> | |
| 32 <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" /> | |
| 33 <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" /> | |
| 34 <param name="ph" size="3" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/> | |
| 35 <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" /> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 38 <data name="output" format="smi"/> | |
| 39 </outputs> | |
| 40 <help> | |
| 41 </help> | |
| 42 </tool> |