Mercurial > repos > bgruening > prepare_ligands_for_docking

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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 11:04:16 +0000
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1 <tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>Tool to prepare ligands for docking with tools like Autodock Vina</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@">0</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 mkdir output && obabel -i '${ligands.ext}' -o '$oformat' -O 'output/molecule.$oformat' -m '$ligands' $gen3d -p $ph_value
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10 ]]></command>
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11 <inputs>
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12 <param type="data" name="ligands" format="sdf,mol2,inchi,smi" label="The ligands which need to be prepared" help="Input in SDF, MOL2, InChi or SMILES format." />
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13 <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
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14 <param name="gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
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15 <param name="oformat" type="select" label="Output format" >
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16 <option value="pdb">PDB</option>
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17 <option value="pdbqt">PDBQT</option>
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18 <option value="mol">MOL</option>
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19 <option value="mol2">MOL2</option>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <collection name="file_outputs" type="list" label="Prepared ligands" >
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24 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
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25 </collection>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
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30 <param name="oformat" value="pdbqt"/>
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31 <param name="ph_value" value="7.4"/>
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32 <output_collection name="file_outputs" type="list" count="10">
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33 <element name="molecule1" file="ob_prepare_ligands1.pdbqt" />
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34 <element name="molecule2" file="ob_prepare_ligands2.pdbqt" />
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35 <!-- we check only the first 2 -->
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36 </output_collection>
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37 </test>
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38 <test>
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39 <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
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40 <param name="oformat" value="mol2"/>
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41 <param name="ph_value" value="7.4"/>
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42 <output_collection name="file_outputs" type="list" count="10">
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43 <element name="molecule1" file="ob_prepare_ligands1.mol2" />
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44 <element name="molecule2" file="ob_prepare_ligands2.mol2" />
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45 <!-- we check only the first 2 -->
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46 </output_collection>
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47 </test>
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48 <test>
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49 <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
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50 <param name="oformat" value="mol"/>
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51 <param name="ph_value" value="7.4"/>
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52 <output_collection name="file_outputs" type="list" count="10">
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53 <!-- just check the count -->
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54 </output_collection>
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55 </test>
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56 <test>
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57 <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
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58 <param name="oformat" value="pdb"/>
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59 <param name="ph_value" value="7.4"/>
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60 <output_collection name="file_outputs" type="list" count="10">
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61 <!-- just check the count -->
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62 </output_collection>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 **What it does?**
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67
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68 This tool uses OpenBabel to convert an input molecule file, typically a SD file, to individual output molecule files in pdbqt, pdb,
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69 mol or mol2 formats. There is one output file for each record in the input.
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70 Protonation is performed at a specified pH and 3D coordinates can optionally be generated. 3D coordinate generation should be used when
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71 the docking program requires 3D structures and the input is not 3D.
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72
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73 The most typical usage is to process a set of ligands in a SD file that will be docked by VINA. In this case the pdbqt output format should
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74 be used, and the resulting collection of molecules can be used as input by VINA.
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75
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76 **Input**
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77
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78 Molecules such as an SD file dataset in history.
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79
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80 **Output**
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81
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82 A collection of individual molecule files in the specified format.
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
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83
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
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84 ]]></help>
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
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85 <expand macro="citations"/>
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
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86 </tool>
06340f46ecb8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
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87