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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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8 obabel
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9 -i"${infile.ext}"
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10 "${infile}
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11 -ocopy
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12 --unique "${descriptor}"
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13 -O "${outfile}"
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14 -e
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15 2>&1
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16 </command>
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17 <inputs>
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18 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/>
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19 <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
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20 <option value="inchi" checked="True">InChI (default)</option>
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21 <option value="cansmi">Canonical SMILES</option>
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22 <option value="cansmiNS">Canonical SMILES (without stereo)</option>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data format_source="infile" name="outfile"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="infile" ftype="smi" value="2_mol.smi"/>
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31 <param name="descriptor" value="inchi" />
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32 <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
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33 </test>
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34 </tests>
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35 <help>
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36
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37 .. class:: infomark
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38
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39 **What does this tool do?**
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40
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41 This tool filters a library of compounds and removes duplicated molecules.
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42
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43 -----
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44
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45 .. class:: warningmark
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46
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47 **Tip:** 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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48
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49 -----
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50
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51 .. class:: infomark
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52
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53 **Output format:** is the same as the input file format.
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54
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55 -----
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56
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57 **This tool uses OpenBabel:** The Open Babel Package, version 2.3.0 http://openbabel.sourceforge.net/
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58
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59 </help>
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60 </tool>
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