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1 <tool id="ctb_remDuplicates" name="Remove duplicated molecules" version="1.0">
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2 <description></description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command>
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2
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8 <![CDATA[
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9 obabel
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10 -i"${infile.ext}"
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11 "${infile}"
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12 -ocopy
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13 --unique "${descriptor}"
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14 -O "${outfile}"
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15 -e
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16 2>&1
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/>
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21 <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
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22 <option value="inchi" checked="True">InChI (default)</option>
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23 <option value="cansmi">Canonical SMILES</option>
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24 <option value="cansmiNS">Canonical SMILES (without stereo)</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format_source="infile" name="outfile"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="infile" ftype="smi" value="2_mol.smi"/>
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33 <param name="descriptor" value="inchi" />
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34 <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
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35 </test>
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36 </tests>
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37 <help>
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38 <![CDATA[
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39
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40 .. class:: infomark
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41
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42 **What this tool does**
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43
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44 Filters a library of compounds and removes duplicated molecules.
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45
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46 -----
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47
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48 .. class:: warningmark
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49
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50 **Hint**
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51
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52 Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms.
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53
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54 -----
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55
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56 .. class:: infomark
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57
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58 **Input**
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59
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60 | - `InChI`_
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61 | - `SMILES Format`_
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62
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63 .. _InChI: http://www.iupac.org/home/publications/e-resources/inchi.html
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64 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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65
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66 -----
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67
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68 .. class:: infomark
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69
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70 **Output**
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71
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72 Same as input format.
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73
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74 -----
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75
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76 .. class:: infomark
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77
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78 **Cite**
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79
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80 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
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81
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82 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
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83
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84 `Open Babel`_
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85
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86 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
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87
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88 ]]>
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89 </help>
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90 </tool>
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