Mercurial > repos > bgruening > openbabel_remduplicates

annotate ob_remDuplicates.xml @ 6:d751e92477ea draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 3ba9268697beb4827bd9e8e639e70166f224cb8b
author bgruening
date Mon, 03 Sep 2018 16:43:39 -0400
parents 75d6c2b7907a
children 65254472e5b4
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75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 <tool id="openbabel_remDuplicates" name="Remove duplicated molecules" version="@VERSION@.0">
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 <description></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-->
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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 detect_errors="aggressive">
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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9 <![CDATA[
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10 obabel
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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11 -i"${infile.ext}"
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 "${infile}"
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13 -ocopy
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14 --unique "${descriptor}"
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15 -O "${outfile}"
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16 -e
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro="infile_all_types"/>
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21 <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
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22 <option value="inchi" selected="True">InChI (default)</option>
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23 <option value="cansmi">Canonical SMILES</option>
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24 <option value="cansmiNS">Canonical SMILES (without stereo)</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <expand macro="output_like_input"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="infile" ftype="smi" value="2_mol.smi"/>
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33 <param name="descriptor" value="inchi" />
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34 <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
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35 </test>
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36 </tests>
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37 <help>
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38 <![CDATA[
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39
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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40 .. class:: infomark
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41
75d6c2b7907a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 **What this tool does**
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43
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44 Filters a library of compounds and removes duplicated molecules.
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45
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46 -----
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47
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48 .. class:: warningmark
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49
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50 **Hint**
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51
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52 Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms.
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53
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54 -----
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55
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56 .. class:: infomark
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57
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58 **Input**
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59
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60 | - `InChI`_
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61 | - `SMILES Format`_
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62
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63 .. _InChI: http://www.iupac.org/home/publications/e-resources/inchi.html
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64 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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65
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66 -----
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67
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68 .. class:: infomark
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70 **Output**
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71
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72 Same as input format.
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73
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75 ]]>
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76 </help>
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77 <expand macro="citations"/>
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78 </tool>