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annotate mol2fps.xml @ 33:73b8c87779ae draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:31:15 -0400
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73b8c87779ae 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">
73b8c87779ae 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>
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 <requirements>
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5 <requirement type="package" version="1.1p1">chemfp</requirement>
73b8c87779ae 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>
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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[
73b8c87779ae 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
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12
73b8c87779ae 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']:
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 ## Open Babel fingerprints
73b8c87779ae 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}'
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 #else:
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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17 ## RDKit fingerprints
73b8c87779ae 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}'
73b8c87779ae 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":
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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20 --RDK
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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21 --fpSize $fp_opts.fpSize
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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22 --minPath $fp_opts.minPath
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 --maxPath $fp_opts.maxPath
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24 --nBitsPerHash $fp_opts.nBitsPerHash
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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25 $fp_opts.useHs
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26 #elif $fp_opts.fp_opts_selector == "--torsions":
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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27 --torsions
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28 --fpSize $fp_opts.fpSize
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29 --targetSize $fp_opts.targetSize
73b8c87779ae 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":
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 --morgan
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32 --fpSize $fp_opts.fpSize
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33 --radius $fp_opts.radius
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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34 $fp_opts.useFeatures
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35 $fp_opts.useChirality
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36 $fp_opts.useBondTypes
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37 #elif $fp_opts.fp_opts_selector == "--pairs":
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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38 --paris
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39 --fpSize $fp_opts.fpSize
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40 --minLength $fp_opts.minLength
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 --maxLength $fp_opts.maxLength
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42 #elif $fp_opts.fp_opts_selector == "--maccs166":
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43 --maccs166
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44 #elif $fp_opts.fp_opts_selector == "--substruct":
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45 --substruct
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46 #end if
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47 #end if
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48 --errors report 2>&1
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49 ]]>
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50 </command>
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51 <inputs>
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52 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
73b8c87779ae 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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54 <param name="fp_opts_selector" type="select" label="Type of fingerprint">
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55 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
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56 <option value='--FP3'>Open Babel FP3 fingerprints</option>
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57 <option value='--FP4'>Open Babel FP4 fingerprints</option>
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58 <option value='--MACCS'>Open Babel MACCS fingerprints</option>
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59 <option value='--RDK'>RDKit topological fingerprint</option>
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60 <option value='--torsions'>RDKit topological Torsion fingerprints</option>
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61 <option value='--morgan'>RDKit Morgan fingerprints</option>
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62 <option value='--pairs'>RDKit Atom Pair fingerprints</option>
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63 <option value='--maccs166'>RDKit MACCS fingerprints</option>
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64 <option value='--substruct'>RDKit substructure fingerprints</option>
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65 </param>
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66 <when value="--FP2" />
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67 <when value="--FP3" />
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68 <when value="--FP4" />
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69 <when value="--MACCS" />
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70 <when value="--RDK">
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71 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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72 <validator type="in_range" min="1" />
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73 </param>
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74 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
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75 <validator type="in_range" min="1" />
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76 </param>
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77 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
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78 <validator type="in_range" min="1" />
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79 </param>
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80 <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
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81 <validator type="in_range" min="1" />
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82 </param>
73b8c87779ae 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"
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
85 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
86 <when value="--torsions">
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
89 </param>
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
92 </param>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
93 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
94 <when value="--morgan">
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
97 </param>
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
100 </param>
73b8c87779ae 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"
73b8c87779ae 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" />
73b8c87779ae 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"
73b8c87779ae 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" />
73b8c87779ae 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"
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
107 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
108 <when value="--pairs">
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
111 </param>
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
114 </param>
73b8c87779ae 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="">
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
117 </param>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
118 </when>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
119 <when value="--maccs166" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
120 <when value="--substruct" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
121 </conditional>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
122
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
123 </inputs>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
124 <outputs>
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
126 </outputs>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
127 <tests>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
128 <!-- FP2 -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
129 <test>
73b8c87779ae 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" />
73b8c87779ae 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" />
73b8c87779ae 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"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
133 </test>
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 <param name="infile" value="CID_2244.smi" ftype="smi" />
73b8c87779ae 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" />
73b8c87779ae 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"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
138 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
139 <!-- FP3 -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
140 <test>
73b8c87779ae 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" />
73b8c87779ae 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" />
73b8c87779ae 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"/>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
144 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
145 <test>
73b8c87779ae 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" />
73b8c87779ae 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" />
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 <!-- FP4 -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
151 <test>
73b8c87779ae 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" />
73b8c87779ae 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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
154 <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
155 </test>
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 <param name="infile" value="CID_2244.smi" ftype="smi" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
158 <param name="fp_opts.fp_opts_selector" value="--FP4" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
159 <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
160 </test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
161 <!-- MACCS -->
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
162 <test>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
163 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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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" />
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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[
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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175
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176 .. class:: infomark
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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::
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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183
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184 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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185 - 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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186
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187 -----
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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188
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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189 .. class:: infomark
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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190
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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191 **Input**
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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192
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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193 FPS fingerprint file format
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194
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195 * Example::
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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196
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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197 - SDF File
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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198
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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199 28434379
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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200 -OEChem-02031205132D
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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201
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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202 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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203 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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204 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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205 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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206 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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207 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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208 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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209 ......
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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210 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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211 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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212 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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213 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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214 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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215 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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216 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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217 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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218 ......
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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 >PUBCHEM_COMPOUND_CID<
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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221 28434379
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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222
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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223 > <PUBCHEM_COMPOUND_CANONICALIZED>
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224 1
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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225
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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226 > <PUBCHEM_CACTVS_COMPLEXITY>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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227 280
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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228
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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229 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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230 2
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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231
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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232 > <PUBCHEM_CACTVS_HBOND_DONOR>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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233 2
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 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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236 2
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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237
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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238 > <PUBCHEM_CACTVS_SUBSKEYS>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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239 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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240
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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241 >
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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242
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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243 - type : FP2
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 -----
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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246
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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247 .. class:: infomark
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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248
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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249 **Output**
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 * Example::
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252
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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260 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
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261 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
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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
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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>