Mercurial > repos > bgruening > chemfp
annotate mol2fps.xml @ 11:92c7cdc243e8 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 70d32dc05d264ffbe03b0c62e54acd5e904c9b7e-dirty"
author | bgruening |
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date | Wed, 24 Jun 2020 13:12:05 -0400 |
parents | 0d88631bb7de |
children | 3b14765c22ee |
rev | line source |
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92c7cdc243e8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 70d32dc05d264ffbe03b0c62e54acd5e904c9b7e-dirty"
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1 <tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="1.6"> |
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0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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2 <description>conversion to several different fingerprint formats</description> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism--> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 <requirements> |
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92c7cdc243e8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 70d32dc05d264ffbe03b0c62e54acd5e904c9b7e-dirty"
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5 <requirement type="package" version="1.6">chemfp</requirement> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 </requirements> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 <command> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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8 <![CDATA[ |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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9 |
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0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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10 #if $fp_opts.fp_opts_selector in ['--FP2', '--FP3', '--FP4', '--MACCS']: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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11 ## Open Babel fingerprints |
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0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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12 ob2fps $fp_opts.fp_opts_selector --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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13 #else: |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 ## RDKit fingerprints |
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0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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15 rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 #if $fp_opts.fp_opts_selector == "--RDK": |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 --RDK |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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18 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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19 --minPath $fp_opts.minPath |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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20 --maxPath $fp_opts.maxPath |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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21 --nBitsPerHash $fp_opts.nBitsPerHash |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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22 $fp_opts.useHs |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 #elif $fp_opts.fp_opts_selector == "--torsions": |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24 --torsions |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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25 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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26 --targetSize $fp_opts.targetSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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27 #elif $fp_opts.fp_opts_selector == "--morgan": |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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28 --morgan |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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29 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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30 --radius $fp_opts.radius |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 $fp_opts.useFeatures |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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32 $fp_opts.useChirality |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33 $fp_opts.useBondTypes |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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34 #elif $fp_opts.fp_opts_selector == "--pairs": |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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35 --pairs |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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36 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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37 --minLength $fp_opts.minLength |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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38 --maxLength $fp_opts.maxLength |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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39 #elif $fp_opts.fp_opts_selector == "--maccs166": |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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40 --maccs166 |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 #elif $fp_opts.fp_opts_selector == "--substruct": |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 --substruct |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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43 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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44 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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45 --errors report 2>&1 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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46 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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47 </command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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48 <inputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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49 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="Molecule file"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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50 <conditional name="fp_opts"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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51 <param name="fp_opts_selector" type="select" label="Type of fingerprint"> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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52 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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53 <option value='--FP3'>Open Babel FP3 fingerprints</option> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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54 <option value='--FP4'>Open Babel FP4 fingerprints</option> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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55 <option value='--MACCS'>Open Babel MACCS fingerprints</option> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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56 <option value='--RDK'>RDKit topological fingerprint</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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57 <option value='--torsions'>RDKit topological Torsion fingerprints</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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58 <option value='--morgan'>RDKit Morgan fingerprints</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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59 <option value='--pairs'>RDKit Atom Pair fingerprints</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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60 <option value='--maccs166'>RDKit MACCS fingerprints</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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61 <option value='--substruct'>RDKit substructure fingerprints</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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62 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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63 <when value="--FP2" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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64 <when value="--FP3" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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65 <when value="--FP4" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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66 <when value="--MACCS" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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67 <when value="--RDK"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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68 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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69 <validator type="in_range" min="1" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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70 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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71 <param name="minPath" type="integer" value="1" label="Minimum number of bonds to include in the subgraph" help=""> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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72 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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73 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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74 <param name="maxPath" type="integer" value="7" label="Maximum number of bonds to include in the subgraph" help=""> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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75 <validator type="in_range" min="1" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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76 </param> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
77 <param name="nBitsPerHash" type="integer" value="4" label="Number of bits to set per path" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
78 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
79 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
80 <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
81 label="Include information about the number of hydrogens on each atom" /> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
82 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
83 <when value="--torsions"> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
84 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
85 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
86 </param> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
87 <param name="targetSize" type="integer" value="4" label="Number of target bits in the fingerprint" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
88 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
89 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
90 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
91 <when value="--morgan"> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
92 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
93 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
94 </param> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
95 <param name="radius" type="integer" value="2" label="Radius for the Morgan algorithm" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
96 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
97 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
98 <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
99 label="Include information about the number of hydrogens on each atom" /> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
100 <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
101 label="Include information about the number of hydrogens on each atom" /> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
102 <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
103 label="Include information about the number of hydrogens on each atom" /> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
104 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
105 <when value="--pairs"> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
106 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
107 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
108 </param> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
109 <param name="minLength" type="integer" value="1" label="Minimum bond count for a pair" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
110 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
111 </param> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
112 <param name="maxLength" type="integer" value="30" label="Maximum bond count for a pair" help=""> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
113 <validator type="in_range" min="1" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
114 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
115 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
116 <when value="--maccs166" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
117 <when value="--substruct" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
118 </conditional> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
119 |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
120 </inputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
121 <outputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
122 <data name="outfile" format="fps" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
123 </outputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
124 <tests> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
125 <!-- FP2 --> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
126 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
127 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
128 <conditional name="fp_opts"> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
129 <param name="fp_opts_selector" value="--FP2" /> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
130 </conditional> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
131 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
132 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
133 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
134 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
135 <conditional name="fp_opts"> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
136 <param name="fp_opts_selector" value="--FP2" /> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
137 </conditional> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
138 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
139 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
140 <!-- FP3 --> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
141 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
142 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
143 <conditional name="fp_opts"> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
144 <param name="fp_opts_selector" value="--FP3" /> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
145 </conditional> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
146 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
147 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
148 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
149 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
7
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
150 <conditional name="fp_opts"> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
151 <param name="fp_opts_selector" value="--FP3" /> |
0d88631bb7de
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
2
diff
changeset
|
152 </conditional> |
2
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
153 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/> |
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154 </test> |
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155 <!-- FP4 --> |
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156 <test> |
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157 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
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158 <conditional name="fp_opts"> |
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159 <param name="fp_opts_selector" value="--FP4" /> |
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160 </conditional> |
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161 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> |
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162 </test> |
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163 <test> |
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164 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
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165 <conditional name="fp_opts"> |
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166 <param name="fp_opts_selector" value="--FP4" /> |
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167 </conditional> |
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168 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> |
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169 </test> |
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170 <!-- MACCS --> |
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171 <test> |
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172 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
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173 <conditional name="fp_opts"> |
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174 <param name="fp_opts_selector" value="--MACCS" /> |
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175 </conditional> |
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176 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> |
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177 </test> |
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178 <test> |
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179 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
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180 <conditional name="fp_opts"> |
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181 <param name="fp_opts_selector" value="--MACCS" /> |
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182 </conditional> |
2
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183 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> |
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184 </test> |
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185 <!-- RDKit2fps --> |
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186 <test> |
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187 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
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188 <conditional name="fp_opts"> |
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189 <param name="fp_opts_selector" value="--torsions" /> |
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190 </conditional> |
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191 <param name="fp_opts.fpSize" value="2048" /> |
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192 <param name="fp_opts.targetSize" value="4" /> |
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193 <output name="outfile" file="CID_2244_torsions.fps" ftype="fps" lines_diff="4"/> |
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194 </test> |
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195 </tests> |
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196 <help> |
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197 <![CDATA[ |
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198 |
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199 .. class:: infomark |
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200 |
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201 **What this tool does** |
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202 |
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203 This tool uses chemfp to calculate molecular fingerprints, supporting a number of common file formats. Chemfp uses OpenBabel, OpenEye and RDKit. |
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204 |
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205 For more information check the websites listed below:: |
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206 |
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207 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity |
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208 - http://openbabel.org/wiki/Tutorial:Fingerprints |
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209 |
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210 ----- |
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211 |
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212 .. class:: infomark |
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213 |
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214 **Input** |
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215 |
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216 FPS fingerprint file format |
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217 |
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218 * Example:: |
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219 |
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220 - SD-File |
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221 |
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222 28434379 |
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223 -OEChem-02031205132D |
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224 |
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225 37 39 0 0 0 0 0 0 0999 V2000 |
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226 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 |
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227 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 |
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228 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 |
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229 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 |
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230 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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231 7.3704 0.9433 0.0000 C 0 0 0 0 |
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232 ...... |
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233 1 15 1 0 0 0 0 |
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234 1 35 1 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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235 2 5 1 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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236 2 11 1 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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237 2 12 1 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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238 3 12 2 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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239 3 13 1 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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240 4 18 1 0 0 0 0 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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241 ...... |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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242 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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243 >PUBCHEM_COMPOUND_CID< |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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244 28434379 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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245 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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246 > <PUBCHEM_COMPOUND_CANONICALIZED> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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247 1 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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248 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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249 > <PUBCHEM_CACTVS_COMPLEXITY> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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250 280 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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251 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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252 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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253 2 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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254 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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255 > <PUBCHEM_CACTVS_HBOND_DONOR> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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256 2 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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257 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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258 > <PUBCHEM_CACTVS_ROTATABLE_BOND> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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259 2 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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260 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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261 > <PUBCHEM_CACTVS_SUBSKEYS> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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262 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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263 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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264 > |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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265 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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266 - type : FP2 |
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267 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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268 ----- |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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269 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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270 .. class:: infomark |
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271 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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272 **Output** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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273 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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274 * Example:: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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275 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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276 #FPS1 |
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277 #num_bits=1021 |
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278 #type=OpenBabel-FP2/1 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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279 #software=OpenBabel/2.3.0 |
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280 #source=/tmp/dataset_409.dat.sdf |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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281 #date=2012-02-03T11:13:39 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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282 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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283 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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284 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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285 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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286 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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287 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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288 </help> |
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289 <citations> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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290 <citation type="doi">10.1186/1758-2946-3-33</citation> |
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291 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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292 <citation type="bibtex"> |
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293 @electronic{rdkit, |
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294 title = {RDKit: Open-source cheminformatics}, |
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295 url ={http://www.rdkit.org} |
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296 } |
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297 </citation> |
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298 </citations> |
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299 </tool> |