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1 <tool id="ctb_subsearch" name="Substructure Search" version="0.1">
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2 <description>of fingerprint data sets</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.2">openbabel</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 <![CDATA[
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8
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9 subsearch.py
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10 -i $query
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11 --iformat "${query.ext}"
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12 --fastsearch-index "${os.path.join($fastsearch.files_path,'molecule.fs')}"
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13 -o "${outfile}"
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14 --oformat $oformat
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15 --max-candidates $max_candidates
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16 --processors "\${GALAXY_SLOTS:-12}"
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17
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/>
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22 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
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23 <param name="max_candidates" size="6" type="integer" value="4000" label="The maximum number of candidates"/>
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24 <param name='oformat' type='select' format='text' label="Output format.">
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25 <option value='smi'>SMILES</option>
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26 <option value='inchi'>InChI</option>
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27 <option value='sdf'>SD-Files</option>
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28 <option value='mol2'>mol2</option>
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29 <option value='names'>Return the molecule names only</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="smi" name="outfile">
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34 <change_format>
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35 <when input="oformat" value="inchi" format="inchi"/>
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36 <when input="oformat" value="sdf" format="sdf"/>
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37 <when input="oformat" value="mol2" format="mol2"/>
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38 <when input="oformat" value="names" format="tabular"/>
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39 </change_format>
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40 </data>
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41 </outputs>
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42 <tests>
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43 <test>
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
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48
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49 .. class:: infomark
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50
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51 **What this tool does**
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52
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53 Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile.
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54
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55 .. _FastSearch: http://openbabel.org/wiki/FastSearch
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56
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57 -----
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58
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59 .. class:: infomark
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60
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61 **Input**
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62
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63 SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES.
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64
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65 -----
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66
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67 .. class:: infomark
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68
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69 **Cite**
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70
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71 `Open Babel`_
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72
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73 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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74
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75 ]]>
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76 </help>
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77 </tool>
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