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annotate subsearch.xml @ 15:9adf3fae2771 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:04:41 +0000
parents 171c94786a56
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171c94786a56 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_subsearch" name="Substructure Search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>of fingerprint data sets</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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11 python '$__tool_directory__/subsearch.py'
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12 -i '${query}'
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13 --iformat '${query.ext}'
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14 --fastsearch-index '${os.path.join($fastsearch.extra_files_path, 'molecule.fs')}'
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15 -o '${outfile}'
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16 --oformat $oformat
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17 --max-candidates $max_candidates
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18 --processors "\${GALAXY_SLOTS:-12}"
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="query" type='data' format="tabular,smi,sdf,inchi,txt" label="Query"/>
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24 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index" help="The OpenBabel fastsearch index can be created with the compound conversion tool."/>
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25 <param name="max_candidates" type="integer" value="4000" label="Maximum number of candidates"/>
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26 <param name='oformat' type='select' format='text' label="Output format">
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27 <option value='smi'>SMILES</option>
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28 <option value='inchi'>InChI</option>
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29 <option value='sdf'>SD-Files</option>
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30 <option value='mol2'>mol2</option>
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31 <option value='names'>Return the molecule names only</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data format="smi" name="outfile">
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36 <change_format>
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37 <when input="oformat" value="inchi" format="inchi"/>
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38 <when input="oformat" value="sdf" format="sdf"/>
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39 <when input="oformat" value="mol2" format="mol2"/>
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40 <when input="oformat" value="names" format="tabular"/>
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41 </change_format>
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42 </data>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="query" ftype="sdf" value="CID_2244.sdf"/>
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47 <param name="fastsearch" value="ob_convert_on_CID2244_obfs.txt" ftype="obfs" >
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48 <composite_data value='molecule.sdf' />
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49 <composite_data value='molecule.fs'/>
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50 </param>
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51 <param name="oformat" value="names" />
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52 <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" />
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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58 .. class:: infomark
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60 **What this tool does**
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62 Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile.
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63
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64 .. _FastSearch: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#substructure-and-similarity-searching
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66 -----
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68 .. class:: infomark
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70 **Input**
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72 SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES.
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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>