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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Tue, 23 Jul 2013 19:00:18 +0200
parents 3d3e7c1d0f49
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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>&#38;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" label="${tool.name} on ${on_string}"/>
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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
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52 .. class:: infomark
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53
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54 **What this tool does**
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56 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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57 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
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59
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60 .. _Obgrep: http://openbabel.org/wiki/Obgrep
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61 .. _here: http://openbabel.org/wiki/SMARTS
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63 -----
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65 .. class:: infomark
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66
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67 **Input**
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68
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69 | - `SD-Format`_
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70 | - `SMILES Format`_
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72 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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73 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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75 -----
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76
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77 .. class:: infomark
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78
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79 **Output**
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80
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81 Same as input format.
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82
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83 -----
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84
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85 .. class:: infomark
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86
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87 **Cite**
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88
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89 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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91 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
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93 `Open Babel`_
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94
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95 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
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97 </help>
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98 </tool>