Mercurial > repos > bgruening > rdock_rbcavity

annotate rbcavity.xml @ 0:06f376dc117a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:34:26 -0400
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children 7e5c2e4bc227
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06f376dc117a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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1 <tool id="rdock_rbcavity" name="rDock cavity definition" version="0.1">
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2 <description>- generate the active site definition needed for rDock docking</description>
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3 <macros>
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4 <import>rdock_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
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8 ln -s '$receptor_prm' ./receptor.prm &&
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9 ln -s '$receptor' receptor.mol2 &&
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10 ln -s '$ligand' ligand.sdf &&
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11 rbcavity -was -d -r receptor.prm
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12 ]]></command>
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13
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14 <configfiles>
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15 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
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16 RECEPTOR_FILE receptor.mol2
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17 RECEPTOR_FLEX 3.0
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18 SECTION MAPPER
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19 SITE_MAPPER RbtLigandSiteMapper
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20 REF_MOL ligand.sdf
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21 RADIUS $radius
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22 SMALL_SPHERE $sphere
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23 MIN_VOLUME $min_volume
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24 MAX_CAVITIES 1
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25 VOL_INCR $vol_incr
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26 GRIDSTEP $gridstep
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27 END_SECTION
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28 SECTION CAVITY
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29 SCORING_FUNCTION RbtCavityGridSF
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30 WEIGHT $weight
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31 END_SECTION
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32 </configfile>
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33 </configfiles>
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34
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35 <inputs>
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36 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (Mol2 format)."/>
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37 <param type="data" name="ligand" format="mol,sdf" label="Reference ligand" help="Single ligand in Mol or SDF format"/>
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38 <param name="radius" type="float" value="6.0" min="0" label="Mapper sphere radius"
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39 help="Mapper radius of large sphere in angstroms; rDock will search for cavities to the small sphere but not to the large sphere"/>
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40 <param name="sphere" type="float" value="1.0" min="0" label="Mapper small sphere radius"
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41 help="Mapper radius of small sphere in angstroms; rDock will search for cavities accessible to the small sphere but not to the large sphere"/>
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42 <param name="min_volume" type="integer" value="100" min="0" label="Mapper minimum volume"
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43 help="Mapper minimum volume in cubic angstroms. rDock will ignore cavities which are smaller than this value"/>
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44 <param name="vol_incr" type="float" value="0.0" min="0" label="Mapper volume increment"
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45 help="Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rDock will temporarily increase the radius of receptor atoms by this amount"/>
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46 <param name="gridstep" type="float" value="0.5" min="0" label="Mapper grid step" help="Grid resolution for mapping in angstroms"/>
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47 <param name="weight" type="float" value="1.0" min="0" label="Cavity weight" help="Cavity weight"/>
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48 </inputs>
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49 <outputs>
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50 <data name="activesite" format="rdock_as" from_work_dir="receptor.as" label="rbcavity active site on ${on_string}"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="receptor" value="receptor.mol2"/>
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55 <param name="ligand" value="ligand.sdf"/>
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56 <output name="activesite" file="receptor.as" compare="sim_size"/>
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57 </test>
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58 <test>
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59 <param name="receptor" value="receptor.mol2"/>
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60 <param name="ligand" value="ligand.mol"/>
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61 <output name="activesite" file="receptor.as" compare="sim_size"/>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65
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66 .. class:: infomark
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67
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68 This tool generates the cavity definition for rDock docking (the receptor.as file) using the rbcavity program.
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69 See http://rdock.sourceforge.net/ for more details about rDock and associated programs.
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70 Only a subset of the parameters are currently exposed. Read the rDock docs for a full understanding.
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72 -----
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73
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74 .. class:: infomark
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76 **Inputs**
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77
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78 1. The protein receptor to dock into as a file in Mol2 format.
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79 2. A reference ligand used to define the location of the active site in Molfile or SDF format.
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80 3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all.
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81
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82 -----
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83
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84 .. class:: infomark
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85
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86 **Outputs**
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87
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88 An active site definition binary file (receptor.as) that is needed by the rDock docking program to guide the docking.
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89
06f376dc117a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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90 ]]></help>
06f376dc117a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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91 <expand macro="citations"/>
06f376dc117a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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92 </tool>