Mercurial > repos > bgruening > openbabel_remduplicates

annotate ob_remDuplicates.xml @ 13:12aca74f07d7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:47:33 +0000
parents 50ca8845e7f5
children
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50ca8845e7f5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_remDuplicates" name="Remove duplicated molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>from a library of compounds</description>
0
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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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50ca8845e7f5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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6 <token name="@GALAXY_VERSION@">0</token>
0
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
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11 obabel
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12 -i"${infile.ext}"
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13 "${infile}"
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14 -ocopy
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15 --unique "${descriptor}"
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16 -O "${outfile}"
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17 -e
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro="infile_all_types"/>
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22 <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
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23 <option value="inchi" selected="True">InChI (default)</option>
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24 <option value="cansmi">Canonical SMILES</option>
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25 <option value="cansmiNS">Canonical SMILES (without stereo)</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <expand macro="output_like_input"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="infile" ftype="smi" value="2_mol.smi"/>
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34 <param name="descriptor" value="inchi" />
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35 <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
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40
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41 .. class:: infomark
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42
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43 **What this tool does**
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45 Filters a library of compounds and removes duplicated molecules.
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46
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47 -----
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48
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49 .. class:: warningmark
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50
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51 **Hint**
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52
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53 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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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 | - `InChI`_
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62 | - `SMILES Format`_
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63
7
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64 .. _InChI: https://en.wikipedia.org/wiki/International_Chemical_Identifier
0
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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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69 .. class:: infomark
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71 **Output**
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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>