annotate multi_obgrep.xml @ 4:e1e344bd8a84 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c84729ec58f7f52d594066158afed175208d3d66
author bgruening
date Wed, 24 May 2017 10:01:44 -0400
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1 <tool id="openbabel_multi_obgrep" name="Multi Compound Search" version="@VERSION@.0">
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2 <description>an advanced molecular grep program using SMARTS</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="aggressive">
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8 <![CDATA[
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9
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10 python $__tool_directory__/multi_obgrep.py
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11 -i $infile
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12 --iformat ${infile.ext}
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13 -q $query
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14 -o "${outfile}"
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15 $invert_matches
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16 --n-times $n_times
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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 --processors "\${GALAXY_SLOTS:-12}"
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21 ]]>
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22 </command>
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23 <inputs>
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24 <expand macro="infile_all_types"/>
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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 <expand macro="output_like_input"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="infile" ftype="smi" value="2_mol.smi"/>
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38 <param name="query" value="pattern.smarts" />
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39 <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" />
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40 </test>
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41 </tests>
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42 <help>
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43 <![CDATA[
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44
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45 .. class:: infomark
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46
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47 **What this tool does**
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48
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49 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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50 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
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51
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52 .. _Obgrep: http://openbabel.org/wiki/Obgrep
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53 .. _here: http://openbabel.org/wiki/SMARTS
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54
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55 -----
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56
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57 .. class:: infomark
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58
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59 **Input**
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60
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61 | - `SD-Format`_
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62 | - `SMILES Format`_
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63
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64 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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65 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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66
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67 -----
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68
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69 .. class:: infomark
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70
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71 **Output**
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72
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73 Same as input format.
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74
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75
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76 ]]>
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77 </help>
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78 <expand macro="citations"/>
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79 </tool>