Mercurial > repos > bgruening > chemfp

annotate mol2fps.xml @ 40:dbd9042bd8c4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 621ba9193927fb8454e915303169276cac764f69"
author bgruening
date Tue, 10 Sep 2019 09:35:01 -0400
parents 02e03ac072cf
children 0a1c281e9224
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1 <tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="1.5">
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2 <description>conversion to several different fingerprint formats</description>
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
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4 <requirements>
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5 <requirement type="package" version="1.5">chemfp</requirement>
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6 <requirement type="package" version="2018.09.3">rdkit</requirement>
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7 <requirement type="package" version="2.4.1">openbabel</requirement>
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8 </requirements>
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9 <command>
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10 <![CDATA[
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11
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12 #if $fp_opts.fp_opts_selector in ['--FP2', '--FP3', '--FP4', '--MACCS']:
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13 ## Open Babel fingerprints
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14 ob2fps $fp_opts.fp_opts_selector --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps'
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15 #else:
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16 ## RDKit fingerprints
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17 rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps'
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18 #if $fp_opts.fp_opts_selector == "--RDK":
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19 --RDK
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20 --fpSize $fp_opts.fpSize
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21 --minPath $fp_opts.minPath
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22 --maxPath $fp_opts.maxPath
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23 --nBitsPerHash $fp_opts.nBitsPerHash
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24 $fp_opts.useHs
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25 #elif $fp_opts.fp_opts_selector == "--torsions":
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26 --torsions
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27 --fpSize $fp_opts.fpSize
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28 --targetSize $fp_opts.targetSize
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29 #elif $fp_opts.fp_opts_selector == "--morgan":
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30 --morgan
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31 --fpSize $fp_opts.fpSize
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32 --radius $fp_opts.radius
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33 $fp_opts.useFeatures
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34 $fp_opts.useChirality
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35 $fp_opts.useBondTypes
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36 #elif $fp_opts.fp_opts_selector == "--pairs":
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37 --pairs
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38 --fpSize $fp_opts.fpSize
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39 --minLength $fp_opts.minLength
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40 --maxLength $fp_opts.maxLength
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41 #elif $fp_opts.fp_opts_selector == "--maccs166":
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42 --maccs166
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43 #elif $fp_opts.fp_opts_selector == "--substruct":
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44 --substruct
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45 #end if
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46 #end if
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47 --errors report 2>&1
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48 ]]>
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49 </command>
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50 <inputs>
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51 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="Molecule file"/>
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52 <conditional name="fp_opts">
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53 <param name="fp_opts_selector" type="select" label="Type of fingerprint">
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54 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
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55 <option value='--FP3'>Open Babel FP3 fingerprints</option>
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56 <option value='--FP4'>Open Babel FP4 fingerprints</option>
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57 <option value='--MACCS'>Open Babel MACCS fingerprints</option>
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58 <option value='--RDK'>RDKit topological fingerprint</option>
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59 <option value='--torsions'>RDKit topological Torsion fingerprints</option>
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60 <option value='--morgan'>RDKit Morgan fingerprints</option>
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61 <option value='--pairs'>RDKit Atom Pair fingerprints</option>
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62 <option value='--maccs166'>RDKit MACCS fingerprints</option>
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63 <option value='--substruct'>RDKit substructure fingerprints</option>
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64 </param>
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65 <when value="--FP2" />
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66 <when value="--FP3" />
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67 <when value="--FP4" />
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68 <when value="--MACCS" />
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69 <when value="--RDK">
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70 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
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71 <validator type="in_range" min="1" />
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72 </param>
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73 <param name="minPath" type="integer" value="1" label="Minimum number of bonds to include in the subgraph" help="">
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74 <validator type="in_range" min="1" />
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75 </param>
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76 <param name="maxPath" type="integer" value="7" label="Maximum number of bonds to include in the subgraph" help="">
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77 <validator type="in_range" min="1" />
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78 </param>
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79 <param name="nBitsPerHash" type="integer" value="4" label="Number of bits to set per path" help="">
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80 <validator type="in_range" min="1" />
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81 </param>
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82 <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true"
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
83 label="Include information about the number of hydrogens on each atom" />
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
84 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
85 <when value="--torsions">
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
86 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
87 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
88 </param>
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
89 <param name="targetSize" type="integer" value="4" label="Number of target bits in the fingerprint" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
90 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
91 </param>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
92 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
93 <when value="--morgan">
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
94 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
95 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
96 </param>
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
97 <param name="radius" type="integer" value="2" label="Radius for the Morgan algorithm" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
98 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
99 </param>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
100 <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false"
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
101 label="Include information about the number of hydrogens on each atom" />
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
102 <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false"
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
103 label="Include information about the number of hydrogens on each atom" />
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
104 <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true"
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
105 label="Include information about the number of hydrogens on each atom" />
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
106 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
107 <when value="--pairs">
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
108 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
109 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
110 </param>
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
111 <param name="minLength" type="integer" value="1" label="Minimum bond count for a pair" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
112 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
113 </param>
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
114 <param name="maxLength" type="integer" value="30" label="Maximum bond count for a pair" help="">
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
115 <validator type="in_range" min="1" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
116 </param>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
117 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
118 <when value="--maccs166" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
119 <when value="--substruct" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
120 </conditional>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
121
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
122 </inputs>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
123 <outputs>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
124 <data name="outfile" format="fps" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
125 </outputs>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
126 <tests>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
127 <!-- FP2 -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
128 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
129 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
130 <conditional name="fp_opts">
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 33
diff changeset
131 <param name="fp_opts_selector" value="--FP2" />
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
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diff changeset
132 </conditional>
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
133 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
134 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
135 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
136 <param name="infile" value="CID_2244.smi" ftype="smi" />
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
137 <conditional name="fp_opts">
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 33
diff changeset
138 <param name="fp_opts_selector" value="--FP2" />
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
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diff changeset
139 </conditional>
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
140 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
141 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
142 <!-- FP3 -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
143 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
144 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
145 <conditional name="fp_opts">
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
146 <param name="fp_opts_selector" value="--FP3" />
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
147 </conditional>
33
73b8c87779ae 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"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
149 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
150 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
151 <param name="infile" value="CID_2244.smi" ftype="smi" />
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
152 <conditional name="fp_opts">
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
153 <param name="fp_opts_selector" value="--FP3" />
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
154 </conditional>
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
155 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
156 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
157 <!-- FP4 -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
158 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
159 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
38
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
160 <conditional name="fp_opts">
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 33
diff changeset
161 <param name="fp_opts_selector" value="--FP4" />
02e03ac072cf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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diff changeset
162 </conditional>
33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
163 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
164 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
165 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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166 <param name="infile" value="CID_2244.smi" ftype="smi" />
38
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167 <conditional name="fp_opts">
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168 <param name="fp_opts_selector" value="--FP4" />
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169 </conditional>
33
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170 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
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171 </test>
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172 <!-- MACCS -->
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173 <test>
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174 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
38
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175 <conditional name="fp_opts">
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176 <param name="fp_opts_selector" value="--MACCS" />
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177 </conditional>
33
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178 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
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179 </test>
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180 <test>
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181 <param name="infile" value="CID_2244.smi" ftype="smi" />
38
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182 <conditional name="fp_opts">
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183 <param name="fp_opts_selector" value="--MACCS" />
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184 </conditional>
33
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185 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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186 </test>
38
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187 <!-- RDKit2fps -->
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188 <test>
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189 <param name="infile" value="CID_2244.smi" ftype="smi" />
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190 <conditional name="fp_opts">
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191 <param name="fp_opts_selector" value="--torsions" />
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192 </conditional>
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193 <param name="fp_opts.fpSize" value="2048" />
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194 <param name="fp_opts.targetSize" value="4" />
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195 <output name="outfile" file="CID_2244_torsions.fps" ftype="fps" lines_diff="4"/>
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196 </test>
33
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197 </tests>
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198 <help>
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199 <![CDATA[
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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200
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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201 .. class:: infomark
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202
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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203 **What this tool does**
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204
38
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205 This tool uses chemfp to calculate molecular fingerprints, supporting a number of common file formats. Chemfp uses OpenBabel, OpenEye and RDKit.
33
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206
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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207 For more information check the websites listed below::
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208
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209 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
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210 - http://openbabel.org/wiki/Tutorial:Fingerprints
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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211
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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212 -----
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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213
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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214 .. class:: infomark
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215
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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216 **Input**
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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217
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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218 FPS fingerprint file format
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219
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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220 * Example::
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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221
38
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222 - SD-File
33
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223
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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224 28434379
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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225 -OEChem-02031205132D
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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226
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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227 37 39 0 0 0 0 0 0 0999 V2000
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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228 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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229 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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230 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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231 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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232 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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233 7.3704 0.9433 0.0000 C 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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234 ......
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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235 1 15 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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236 1 35 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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237 2 5 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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238 2 11 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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239 2 12 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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240 3 12 2 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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241 3 13 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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242 4 18 1 0 0 0 0
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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243 ......
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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244
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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245 >PUBCHEM_COMPOUND_CID<
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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246 28434379
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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247
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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248 > <PUBCHEM_COMPOUND_CANONICALIZED>
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249 1
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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250
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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251 > <PUBCHEM_CACTVS_COMPLEXITY>
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252 280
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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253
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254 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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255 2
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256
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257 > <PUBCHEM_CACTVS_HBOND_DONOR>
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258 2
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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259
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260 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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261 2
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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262
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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263 > <PUBCHEM_CACTVS_SUBSKEYS>
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264 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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265
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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266 >
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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267
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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268 - type : FP2
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269
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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270 -----
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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271
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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272 .. class:: infomark
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273
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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274 **Output**
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275
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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276 * Example::
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277
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278 #FPS1
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279 #num_bits=1021
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280 #type=OpenBabel-FP2/1
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281 #software=OpenBabel/2.3.0
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282 #source=/tmp/dataset_409.dat.sdf
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283 #date=2012-02-03T11:13:39
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284 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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285 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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286 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
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287
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288
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289 ]]>
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290 </help>
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291 <citations>
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292 <citation type="doi">10.1186/1758-2946-3-33</citation>
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293 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
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294 <citation type="bibtex">
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295 @electronic{rdkit,
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296 title = {RDKit: Open-source cheminformatics},
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297 url ={http://www.rdkit.org}
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298 }
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299 </citation>
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300 </citations>
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301 </tool>