Mercurial > repos > bgruening > openbabel_obgrep

annotate ob_grep.xml @ 0:b0311f002a5f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
author bgruening
date Sat, 20 May 2017 08:59:45 -0400
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b0311f002a5f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
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1 <tool id="openbabel_obgrep" name="Compound Search" version="@VERSION@.0">
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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 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command>
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9 <![CDATA[
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10 obgrep
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11 $invert_matches
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12 #if $n_times:
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13 -t $n_times
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14 #end if
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15 $only_name
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16 $full_match
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17 $number_of_matches
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18 -i '${infile.ext}'
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19 '${smarts_pattern}'
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20 '${infile}'
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21 > '${outfile}'
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22 ]]>
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23 </command>
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24 <inputs>
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25 <expand macro="infile_all_types"/>
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26 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
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27 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
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28 <param name="n_times" type="integer" value="" min="1" optional="True"
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29 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 <expand macro="output_like_input"/>
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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="False" />
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43 <param name="only_name" value="False" />
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44 <param name="full_match" value="False" />
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45 <param name="number_of_matches" value="False" />
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46 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
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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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55
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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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58
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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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62
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63 -----
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64
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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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71
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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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74
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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 </help>
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85 <expand macro="citations"/>
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86 </tool>