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1 <tool id="ctb_multi_obgrep" name="Multi Compound Search" version="0.1">
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2 <description>an advanced molecular grep program using SMARTS</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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2
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7 <![CDATA[
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8
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9 multi_obgrep.py
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10 -i $infile
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11 --iformat ${infile.ext}
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12 -q $query
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13 -o "${outfile}"
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14 $invert_matches
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15 --n-times $n_times
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16 $only_name
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17 $full_match
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18 $number_of_matches
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19 --processors "\${GALAXY_SLOTS:-12}"
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20
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2
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
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25 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
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26 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
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27 <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
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28 <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" />
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29 <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern (-f)" truevalue="--full-match" falsevalue="" checked="false" />
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30 <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
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31 </inputs>
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32 <outputs>
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33 <data name="outfile" format_source="infile" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 </test>
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38 </tests>
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39 <help>
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2
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40 <![CDATA[
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41
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42 .. class:: infomark
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43
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44 **What this tool does**
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45
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46 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
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47 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
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48
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49 .. _Obgrep: http://openbabel.org/wiki/Obgrep
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50 .. _here: http://openbabel.org/wiki/SMARTS
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51
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52 -----
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53
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54 .. class:: infomark
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55
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56 **Input**
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57
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58 | - `SD-Format`_
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59 | - `SMILES Format`_
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60
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61 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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62 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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63
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64 -----
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65
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66 .. class:: infomark
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67
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68 **Output**
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69
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70 Same as input format.
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71
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72 -----
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73
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74 .. class:: infomark
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75
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76 **Cite**
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77
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78 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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79
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80 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
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81
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82 `Open Babel`_
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83
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84 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
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85
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2
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86 ]]>
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87 </help>
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88 </tool>
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