Mercurial > repos > bgruening > chemfp
diff chemfp_ob2fps/ob2fps.xml @ 6:438bc12d591b
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 26 Apr 2013 08:02:45 -0400 |
| parents | a8ac5250d59c |
| children |
line wrap: on
line diff
--- a/chemfp_ob2fps/ob2fps.xml Tue Apr 02 05:26:28 2013 -0400 +++ b/chemfp_ob2fps/ob2fps.xml Fri Apr 26 08:02:45 2013 -0400 @@ -1,20 +1,116 @@ -<tool id="chemfp_ob2fps" name="Molecules to Fingerprints" version="0.1.2"> +<tool id="chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0"> <description>with different fingerprint types</description> <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> <requirements> <requirement type="package" version="1.1p1">chemfp</requirement> + <requirement type="package" version="2012_12_1">rdkit</requirement> </requirements> <command> - ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1 + #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']: + ## Open Babel fingerprints + ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1 + #else: + ## RDKit fingerprints + rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}" + #if $fp_opts.fp_opts_selector=="--RDK": + --RDK + --fpSize $fp_opts.fpSize + --minPath $fp_opts.minPath + --maxPath $fp_opts.maxPath + --nBitsPerHash $fp_opts.nBitsPerHash + $fp_opts.useHs + #elif $fp_opts.fp_opts_selector=="--torsions": + --torsions + --fpSize $fp_opts.fpSize + --targetSize $fp_opts.targetSize + #elif $fp_opts.fp_opts_selector=="--morgan": + --morgan + --fpSize $fp_opts.fpSize + --radius $fp_opts.radius + $fp_opts.useFeatures + $fp_opts.useChirality + $fp_opts.useBondTypes + #elif $fp_opts.fp_opts_selector=="--pairs": + --paris + --fpSize $fp_opts.fpSize + --minLength $fp_opts.minLength + --maxLength $fp_opts.maxLength + #elif $fp_opts.fp_opts_selector=="--maccs166": + --maccs166 + #elif $fp_opts.fp_opts_selector=="--substruct": + --substruct + #endif + --errors report 2>&1 + #endif </command> <inputs> <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/> - <param name='fptype' type='select' format='text'> - <option value='--FP2'>FP2</option> - <option value='--FP3'>FP3</option> - <option value='--FP4'>FP4</option> - <option value='--MACCS'>MACCS</option> - </param> + <conditional name="fp_opts"> + <param name="fp_opts_selector" type="select" label="Type of fingerprint"> + <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option> + <option value='--FP3'>Open Babel FP3 fingerprints</option> + <option value='--FP4'>Open Babel FP4 fingerprints</option> + <option value='--MACCS'>Open Babel MACCS fingerprints</option> + <option value='--RDK'>RDKit topological fingerprint</option> + <option value='--torsions'>RDKit topological Torsion fingerprints</option> + <option value='--morgan'>RDKit Morgan fingerprints</option> + <option value='--pairs'>RDKit Atom Pair fingerprints</option> + <option value='--maccs166'>RDKit MACCS fingerprints</option> + <option value='--substruct'>RDKit substructure fingerprints</option> + </param> + <when value="--FP2" /> + <when value="--FP3" /> + <when value="--FP4" /> + <when value="--MACCS" /> + <when value="--RDK"> + <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="useHs" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" /> + </when> + <when value="--torsions"> + <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help=""> + <validator type="in_range" min="1" /> + </param> + </when> + <when value="--morgan"> + <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="useFeatures" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" /> + <param name="useChirality" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" /> + <param name="useBondTypes" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" /> + </when> + <when value="--pairs"> + <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help=""> + <validator type="in_range" min="1" /> + </param> + </when> + <when value="--maccs166" /> + <when value="--substruct" /> + </conditional> + </inputs> <outputs> <data name="outfile" format="fps" />