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1 <tool id="ctb_obgrep" name="Compound Search" version="0.1">
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2 <description>an advanced molecular grep program using SMARTS</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 ## The command is a Cheetah template which allows some Python based syntax.
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9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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10 obgrep
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11
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12 $invert_matches
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13 #if $n_times != 0:
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14 -t $n_times
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15 #end if
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16
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17 $only_name
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18 $full_match
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19 $number_of_matches
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20 -i ${infile.ext}
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21 "${smarts_pattern}"
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22 "${infile}"
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23 > "${outfile}" 2>&1
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24 </command>
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25 <inputs>
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26 <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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27 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
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28 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
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29 <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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30 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
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31 <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" truevalue="-f" falsevalue="" checked="false" />
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32 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
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33 </inputs>
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34 <options sanitize="False"/>
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35 <outputs>
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36 <data name="outfile" format_source="infile" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="infile" ftype="smi" value="8_mol.smi"/>
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41 <param name="smarts_pattern" value="CO"/>
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42 <param name="invert_matches" value="" />
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43 <param name="n_times" value="0"/>
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44 <param name="only_name" value="" />
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45 <param name="full_match" value="" />
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46 <param name="number_of_matches" value="" />
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47 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
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48 </test>
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49 </tests>
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50 <help>
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51 .. class:: warningmark
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52
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53 **What it does**
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54
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55 The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.
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56
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57 -----
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58
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59 **Output format**
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60
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61
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62 **References**
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63
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64 Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck, Joerg Kurt Wegner, Egon Willighagen. "The Blue Obelisk -- Interoperability in Chemical Informatics." J. Chem. Inf. Model. (2006) 46(3) 991-998. DOI:10.1021/ci050400b
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65 The Open Babel Package http://openbabel.sourceforge.net/
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66
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67 </help>
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68 </tool>
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