Mercurial > repos > bgruening > chemfp
annotate mol2fps.xml @ 2:70b071de9bee draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author | bgruening |
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date | Sat, 20 May 2017 08:31:44 -0400 |
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children | 0d88631bb7de |
rev | line source |
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70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 <tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0"> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 <description>with different fingerprint types</description> |
70b071de9bee
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> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 <requirement type="package" version="1.1p1">chemfp</requirement> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 <requirement type="package" version="2016.03.3">rdkit</requirement> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 <requirement type="package" version="2.4.1">openbabel</requirement> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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8 </requirements> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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9 <command> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 <![CDATA[ |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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11 #set $fptype = $fp_opts.fp_opts_selector |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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13 #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']: |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 ## Open Babel fingerprints |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 ob2fps $fptype --in '${infile.ext}' '${infile}' -o '${outfile}' |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 #else: |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 ## RDKit fingerprints |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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18 rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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19 #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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20 --RDK |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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21 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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22 --minPath $fp_opts.minPath |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 --maxPath $fp_opts.maxPath |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24 --nBitsPerHash $fp_opts.nBitsPerHash |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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25 $fp_opts.useHs |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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26 #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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27 --torsions |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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28 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 --targetSize $fp_opts.targetSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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30 #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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31 --morgan |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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32 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33 --radius $fp_opts.radius |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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34 $fp_opts.useFeatures |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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35 $fp_opts.useChirality |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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36 $fp_opts.useBondTypes |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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37 #elif $fp_opts.fp_opts_selector == "--pairs": |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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38 --paris |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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39 --fpSize $fp_opts.fpSize |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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40 --minLength $fp_opts.minLength |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 --maxLength $fp_opts.maxLength |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 #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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43 --maccs166 |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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44 #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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45 --substruct |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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46 #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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47 #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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48 --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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49 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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50 </command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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51 <inputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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52 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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53 <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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54 <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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55 <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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56 <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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57 <option value='--FP4'>Open Babel FP4 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='--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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59 <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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60 <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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61 <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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62 <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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63 <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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64 <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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65 </param> |
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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="--FP2" /> |
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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="--FP3" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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68 <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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69 <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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70 <when value="--RDK"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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71 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> |
70b071de9bee
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" /> |
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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 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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74 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help=""> |
70b071de9bee
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> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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77 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help=""> |
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="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help=""> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
81 <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
|
82 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
83 <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
84 label="include information about the number of hydrogens on each atom" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
85 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
86 <when value="--torsions"> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
87 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> |
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 <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help=""> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
91 <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
|
92 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
93 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
94 <when value="--morgan"> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
95 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> |
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="radius" type="integer" value="2" label="radius for the Morgan algorithm" help=""> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
99 <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
|
100 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
101 <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
102 label="include information about the number of hydrogens on each atom" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
103 <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
104 label="include information about the number of hydrogens on each atom" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
105 <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
106 label="include information about the number of hydrogens on each atom" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
107 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
108 <when value="--pairs"> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
109 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> |
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> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
112 <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help=""> |
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 <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help=""> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
116 <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
|
117 </param> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
118 </when> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
119 <when value="--maccs166" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
120 <when value="--substruct" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
121 </conditional> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
122 |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
123 </inputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
124 <outputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
125 <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
|
126 </outputs> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
127 <tests> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
128 <!-- FP2 --> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
129 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
130 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
131 <param name="fp_opts.fp_opts_selector" value="--FP2" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
132 <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
|
133 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
134 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
135 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
136 <param name="fp_opts.fp_opts_selector" value="--FP2" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
137 <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
|
138 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
139 <!-- FP3 --> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
140 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
141 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
142 <param name="fp_opts.fp_opts_selector" value="--FP3" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
143 <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
|
144 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
145 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
146 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
147 <param name="fp_opts.fp_opts_selector" value="--FP3" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
148 <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
|
149 </test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
150 <!-- FP4 --> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
151 <test> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
152 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
153 <param name="fp_opts.fp_opts_selector" value="--FP4" /> |
70b071de9bee
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
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154 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> |
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155 </test> |
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156 <test> |
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157 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
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158 <param name="fp_opts.fp_opts_selector" value="--FP4" /> |
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159 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> |
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160 </test> |
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161 <!-- MACCS --> |
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162 <test> |
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163 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> |
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164 <param name="fp_opts.fp_opts_selector" value="--MACCS" /> |
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165 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> |
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166 </test> |
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167 <test> |
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168 <param name="infile" value="CID_2244.smi" ftype="smi" /> |
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169 <param name="fp_opts.fp_opts_selector" value="--MACCS" /> |
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170 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> |
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171 </test> |
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172 </tests> |
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173 <help> |
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174 <![CDATA[ |
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175 |
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176 .. class:: infomark |
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177 |
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178 **What this tool does** |
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179 |
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180 This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_. |
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181 |
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182 For more information check the websites listed below:: |
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183 |
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184 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity |
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185 - http://openbabel.org/wiki/Tutorial:Fingerprints |
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186 |
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187 ----- |
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188 |
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189 .. class:: infomark |
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190 |
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191 **Input** |
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192 |
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193 FPS fingerprint file format |
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194 |
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195 * Example:: |
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196 |
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197 - SDF File |
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198 |
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199 28434379 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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200 -OEChem-02031205132D |
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201 |
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202 37 39 0 0 0 0 0 0 0999 V2000 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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203 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 |
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204 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 |
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205 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 |
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206 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 |
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207 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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208 7.3704 0.9433 0.0000 C 0 0 0 0 |
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209 ...... |
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210 1 15 1 0 0 0 0 |
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211 1 35 1 0 0 0 0 |
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212 2 5 1 0 0 0 0 |
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213 2 11 1 0 0 0 0 |
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214 2 12 1 0 0 0 0 |
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215 3 12 2 0 0 0 0 |
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216 3 13 1 0 0 0 0 |
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217 4 18 1 0 0 0 0 |
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218 ...... |
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219 |
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220 >PUBCHEM_COMPOUND_CID< |
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221 28434379 |
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222 |
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223 > <PUBCHEM_COMPOUND_CANONICALIZED> |
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224 1 |
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225 |
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226 > <PUBCHEM_CACTVS_COMPLEXITY> |
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227 280 |
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228 |
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229 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> |
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230 2 |
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231 |
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232 > <PUBCHEM_CACTVS_HBOND_DONOR> |
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233 2 |
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234 |
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235 > <PUBCHEM_CACTVS_ROTATABLE_BOND> |
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236 2 |
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237 |
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238 > <PUBCHEM_CACTVS_SUBSKEYS> |
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239 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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240 |
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241 > |
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242 |
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243 - type : FP2 |
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244 |
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245 ----- |
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246 |
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247 .. class:: infomark |
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248 |
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249 **Output** |
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250 |
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251 * Example:: |
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252 |
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253 #FPS1 |
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254 #num_bits=1021 |
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255 #type=OpenBabel-FP2/1 |
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256 #software=OpenBabel/2.3.0 |
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257 #source=/tmp/dataset_409.dat.sdf |
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258 #date=2012-02-03T11:13:39 |
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259 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c |
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260 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300 |
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261 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379 |
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262 |
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263 |
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264 ]]> |
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265 </help> |
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266 <citations> |
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267 <citation type="doi">10.1186/1758-2946-3-33</citation> |
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268 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> |
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269 <citation type="bibtex"> |
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270 @electronic{rdkit, |
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271 title = {RDKit: Open-source cheminformatics}, |
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272 url ={http://www.rdkit.org} |
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273 } |
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274 </citation> |
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275 </citations> |
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276 </tool> |