annotate CADDSuite-1.6/galaxyconfigs/tool_conf.xml @ 8:dbb480e39d95 draft

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<?xml version="1.0"?>
<toolbox>
  <label text="CADDSuite 1.6" id="cadds" />

  <section name="Get Data" id="getext">
    <tool file="CADDSuite/galaxyconfigs/tools/upload.xml"/>
    <tool file="CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml"/>
    <tool file="CADDSuite/galaxyconfigs/tools/PDBDownload.xml"/>
    <tool file="CADDSuite/galaxyconfigs/tools/DBExporter.xml"/>
  </section>

  <section name="Data preparation" id="dataPrep">
	<tool file="CADDSuite/galaxyconfigs/tools/PDBCutter.xml" />
	<tool file="CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml" />
	<tool file="CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml" />
	<tool file="CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml" />
   <tool file="CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml"/>
   <tool file="CADDSuite/galaxyconfigs/tools/EvenSplit.xml"/>
   <tool file="CADDSuite/galaxyconfigs/tools/PropertyModifier.xml"/>
   <tool file="CADDSuite/galaxyconfigs/tools/MolFilter.xml"/>
  </section>

  <section name="Checks and evaluations" id="checks">
	<tool file="CADDSuite/galaxyconfigs/tools/ProteinCheck.xml" />
	<tool file="CADDSuite/galaxyconfigs/tools/LigCheck.xml" />
  </section>

	<section name="QSAR" id="queasy">
		<tool file="CADDSuite/galaxyconfigs/tools/InputReader.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/ModelCreator.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/FeatureSelector.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/Validator.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/MolPredictor.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/AutoModel.xml" />
	</section>

  <section name="Docking" id="dockingTools">
	 <tool file="CADDSuite/galaxyconfigs/tools/WaterFinder.xml" />
	 <tool file="CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml" />
	 <tool file="CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml" />
	 <tool file="CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml"/>
	 <tool file="CADDSuite/galaxyconfigs/tools/PocketDetector.xml"/>
    <tool file="CADDSuite/galaxyconfigs/tools/GridBuilder.xml" />
    <tool file="CADDSuite/galaxyconfigs/tools/IMGDock.xml" />
  </section>

  <section name="Rescoring" id="rescoringsection">
	<tool file="CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml"/>
	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes-train.xml"/>
	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes.xml"/>
	<tool file="CADDSuite/galaxyconfigs/tools/PocketCutter.xml"/>
	<tool file="CADDSuite/galaxyconfigs/tools/SurfaceMatcher.xml" />
	<tool file="CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml" />
  </section>

   <section name="Off-target search" id="offtargets">
	<tool file="CADDSuite/galaxyconfigs/tools/PocketCutter.xml"/>
	<tool file="CADDSuite/galaxyconfigs/tools/SurfaceMatcher.xml" />
  </section>

	<section name="Analysis" id="analysis">
		<tool file="CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml"/>
		<tool file="CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml"/>
		<tool file="CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml"/>
		<tool file="CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml"/>
	</section>

	<section name="Convert, combine and store" id="storeData">
		<tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/MolCombine.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/DockResultMerger.xml"/>
		<tool file="CADDSuite/galaxyconfigs/tools/Filter.xml"/>
		<tool file="CADDSuite/galaxyconfigs/tools/MolDepict.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/DBImporter.xml" />
		<tool file="CADDSuite/galaxyconfigs/tools/VendorFinder.xml" />
	</section>

</toolbox>