Mercurial > repos > marcel > caddsuite_linux_x86_64
changeset 5:b7a89b15646f
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--- a/CADDSuite/AntitargetRescorer Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/AntitargetRescorer Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/AntitargetRescorer.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/AntitargetRescorer.bin "$@"
--- a/CADDSuite/AutoModel Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/AutoModel Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/AutoModel.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/AutoModel.bin "$@"
--- a/CADDSuite/BindingDBCleaner Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/BindingDBCleaner Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/BindingDBCleaner.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/BindingDBCleaner.bin "$@"
--- a/CADDSuite/CADDSuite-description.txt Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/CADDSuite-description.txt Tue Jul 12 10:23:33 2011 -0400 @@ -31,10 +31,11 @@ Docking: - WaterFinder: find strongly bound water molecules - SpatialConstraintDefiner: define spatial constraint + - InteractionConstraintDefiner: define interaction constraint - ConstraintsFinder: find strongly interacting residues - PocketDetector: detect ligand binding pocket - GridBuilder: precalculate grids for docking - - IMeedyDock: run Iterative Multi-Greedy Docking + - IMGDock: run Iterative Multi-Greedy Docking Rescoring: - SimpleRescorer: rescore docking results
--- a/CADDSuite/CombiLibGenerator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/CombiLibGenerator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/CombiLibGenerator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/CombiLibGenerator.bin "$@"
--- a/CADDSuite/ConstraintsFinder Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/ConstraintsFinder Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ConstraintsFinder.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ConstraintsFinder.bin "$@"
--- a/CADDSuite/Converter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/Converter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Converter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Converter.bin "$@"
--- a/CADDSuite/DBExporter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/DBExporter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/DBExporter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/DBExporter.bin "$@"
--- a/CADDSuite/DBImporter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/DBImporter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/DBImporter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/DBImporter.bin "$@"
--- a/CADDSuite/DockResultMerger Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/DockResultMerger Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/DockResultMerger.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/DockResultMerger.bin "$@"
--- a/CADDSuite/EvenSplit Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/EvenSplit Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/EvenSplit.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/EvenSplit.bin "$@"
--- a/CADDSuite/FeatureSelector Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/FeatureSelector Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/FeatureSelector.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/FeatureSelector.bin "$@"
--- a/CADDSuite/GalaxyConfigGenerator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/GalaxyConfigGenerator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@"
--- a/CADDSuite/GridBuilder Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/GridBuilder Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/GridBuilder.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/GridBuilder.bin "$@"
--- a/CADDSuite/IMGDock Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/IMGDock Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/IMGDock.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/IMGDock.bin "$@"
--- a/CADDSuite/InputPartitioner Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/InputPartitioner Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InputPartitioner.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/InputPartitioner.bin "$@"
--- a/CADDSuite/InputReader Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/InputReader Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InputReader.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/InputReader.bin "$@"
--- a/CADDSuite/InteractionConstraintDefiner Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/InteractionConstraintDefiner Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@"
--- a/CADDSuite/LigCheck Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/LigCheck Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/LigCheck.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/LigCheck.bin "$@"
--- a/CADDSuite/Ligand3DGenerator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/Ligand3DGenerator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Ligand3DGenerator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Ligand3DGenerator.bin "$@"
--- a/CADDSuite/LigandFileSplitter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/LigandFileSplitter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/LigandFileSplitter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/LigandFileSplitter.bin "$@"
--- a/CADDSuite/ModelCreator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/ModelCreator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ModelCreator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ModelCreator.bin "$@"
--- a/CADDSuite/MolCombine Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/MolCombine Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolCombine.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolCombine.bin "$@"
--- a/CADDSuite/MolDepict Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/MolDepict Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolDepict.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolDepict.bin "$@"
--- a/CADDSuite/MolFilter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/MolFilter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolFilter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolFilter.bin "$@"
--- a/CADDSuite/MolPredictor Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/MolPredictor Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolPredictor.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolPredictor.bin "$@"
--- a/CADDSuite/PDBCutter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/PDBCutter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PDBCutter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PDBCutter.bin "$@"
--- a/CADDSuite/PDBDownload Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/PDBDownload Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PDBDownload.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PDBDownload.bin "$@"
--- a/CADDSuite/PartialChargesCopy Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/PartialChargesCopy Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PartialChargesCopy.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PartialChargesCopy.bin "$@"
--- a/CADDSuite/PocketDetector Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/PocketDetector Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PocketDetector.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PocketDetector.bin "$@"
--- a/CADDSuite/Predictor Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/Predictor Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Predictor.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Predictor.bin "$@"
--- a/CADDSuite/PropertyModifier Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/PropertyModifier Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PropertyModifier.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PropertyModifier.bin "$@"
--- a/CADDSuite/PropertyPlotter Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/PropertyPlotter Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PropertyPlotter.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PropertyPlotter.bin "$@"
--- a/CADDSuite/ProteinCheck Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/ProteinCheck Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ProteinCheck.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ProteinCheck.bin "$@"
--- a/CADDSuite/ProteinProtonator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/ProteinProtonator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ProteinProtonator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ProteinProtonator.bin "$@"
--- a/CADDSuite/QuEasyRun Tue Jun 28 10:37:20 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/QuEasyRun.bin "$@"
--- a/CADDSuite/README Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/README Tue Jul 12 10:23:33 2011 -0400 @@ -7,7 +7,7 @@ For an overview over the contained tools, please see CADDSuite-description.txt. After extraction the package, you can directly start the applications using the startup-scripts in the base-folder. -For more information about an individual tool, please call the tool without any parameters (or with '-h'). +For more information about an individual tool, please call the tool without any parameters (or with '-help').
--- a/CADDSuite/RMSDCalculator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/RMSDCalculator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/RMSDCalculator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/RMSDCalculator.bin "$@"
--- a/CADDSuite/ScoreAnalyzer Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/ScoreAnalyzer Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ScoreAnalyzer.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ScoreAnalyzer.bin "$@"
--- a/CADDSuite/SideChainGridBuilder Tue Jun 28 10:37:20 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SideChainGridBuilder.bin "$@"
--- a/CADDSuite/SimilarityAnalyzer Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/SimilarityAnalyzer Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@"
--- a/CADDSuite/SimpleRescorer Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/SimpleRescorer Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SimpleRescorer.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SimpleRescorer.bin "$@"
--- a/CADDSuite/SpatialConstraintDefiner Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/SpatialConstraintDefiner Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@"
--- a/CADDSuite/TaGRes Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/TaGRes Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/TaGRes.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/TaGRes.bin "$@"
--- a/CADDSuite/TaGRes-train Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/TaGRes-train Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/TaGRes-train.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/TaGRes-train.bin "$@"
--- a/CADDSuite/Validator Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/Validator Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Validator.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Validator.bin "$@"
--- a/CADDSuite/VendorFinder Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/VendorFinder Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/VendorFinder.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/VendorFinder.bin "$@"
--- a/CADDSuite/WaterFinder Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/WaterFinder Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ #!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/WaterFinder.bin "$@" + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/WaterFinder.bin "$@"
--- a/CADDSuite/changelog.txt Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/changelog.txt Tue Jul 12 10:23:33 2011 -0400 @@ -1,3 +1,11 @@ +Version 0.95, 07-12-2011: + - Let rescoring search for correct LigCheck molecule property-tags + - Indicate optional parameters in galaxy interface + - Fixed compilation with disabled QuEasyViz + - Added missing gnuplot data file to release archive + - Set some default values for flags for use in GUIs + - Clarified EvenSplit docu + Version 0.94, 06-27-2011: - Fixed tool-startup script for pathes containing whitespaces - New tool SpatialConstraintDefiner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/gnuplot/prologue.ps Tue Jul 12 10:23:33 2011 -0400 @@ -0,0 +1,371 @@ +% +% Gnuplot Prolog Version 4.4 (January 2010) +% +%/SuppressPDFMark true def +% +/M {moveto} bind def +/L {lineto} bind def +/R {rmoveto} bind def +/V {rlineto} bind def +/N {newpath moveto} bind def +/Z {closepath} bind def +/C {setrgbcolor} bind def +/f {rlineto fill} bind def +/Gshow {show} def % May be redefined later in the file to support UTF-8 +/vpt2 vpt 2 mul def +/hpt2 hpt 2 mul def +/Lshow {currentpoint stroke M 0 vshift R + Blacktext {gsave 0 setgray show grestore} {show} ifelse} def +/Rshow {currentpoint stroke M dup stringwidth pop neg vshift R + Blacktext {gsave 0 setgray show grestore} {show} ifelse} def +/Cshow {currentpoint stroke M dup stringwidth pop -2 div vshift R + Blacktext {gsave 0 setgray show grestore} {show} ifelse} def +/UP {dup vpt_ mul /vpt exch def hpt_ mul /hpt exch def + /hpt2 hpt 2 mul def /vpt2 vpt 2 mul def} def +/DL {Color {setrgbcolor Solid {pop []} if 0 setdash} + {pop pop pop 0 setgray Solid {pop []} if 0 setdash} ifelse} def +/BL {stroke userlinewidth 2 mul setlinewidth + Rounded {1 setlinejoin 1 setlinecap} if} def +/AL {stroke userlinewidth 2 div setlinewidth + Rounded {1 setlinejoin 1 setlinecap} if} def +/UL {dup gnulinewidth mul /userlinewidth exch def + dup 1 lt {pop 1} if 10 mul /udl exch def} def +/PL {stroke userlinewidth setlinewidth + Rounded {1 setlinejoin 1 setlinecap} if} def +% Default Line colors +/LCw {1 1 1} def +/LCb {0 0 0} def +/LCa {0 0 0} def +/LC0 {1 0 0} def +/LC1 {0 1 0} def +/LC2 {0 0 1} def +/LC3 {1 0 1} def +/LC4 {0 1 1} def +/LC5 {1 1 0} def +/LC6 {0 0 0} def +/LC7 {1 0.3 0} def +/LC8 {0.5 0.5 0.5} def +% Default Line Types +/LTw {PL [] 1 setgray} def +/LTb {BL [] LCb DL} def +/LTa {AL [1 udl mul 2 udl mul] 0 setdash LCa setrgbcolor} def +/LT0 {PL [] LC0 DL} def +/LT1 {PL [4 dl1 2 dl2] LC1 DL} def +/LT2 {PL [2 dl1 3 dl2] LC2 DL} def +/LT3 {PL [1 dl1 1.5 dl2] LC3 DL} def +/LT4 {PL [6 dl1 2 dl2 1 dl1 2 dl2] LC4 DL} def +/LT5 {PL [3 dl1 3 dl2 1 dl1 3 dl2] LC5 DL} def +/LT6 {PL [2 dl1 2 dl2 2 dl1 6 dl2] LC6 DL} def +/LT7 {PL [1 dl1 2 dl2 6 dl1 2 dl2 1 dl1 2 dl2] LC7 DL} def +/LT8 {PL [2 dl1 2 dl2 2 dl1 2 dl2 2 dl1 2 dl2 2 dl1 4 dl2] LC8 DL} def +/Pnt {stroke [] 0 setdash gsave 1 setlinecap M 0 0 V stroke grestore} def +/Dia {stroke [] 0 setdash 2 copy vpt add M + hpt neg vpt neg V hpt vpt neg V + hpt vpt V hpt neg vpt V closepath stroke + Pnt} def +/Pls {stroke [] 0 setdash vpt sub M 0 vpt2 V + currentpoint stroke M + hpt neg vpt neg R hpt2 0 V stroke + } def +/Box {stroke [] 0 setdash 2 copy exch hpt sub exch vpt add M + 0 vpt2 neg V hpt2 0 V 0 vpt2 V + hpt2 neg 0 V closepath stroke + Pnt} def +/Crs {stroke [] 0 setdash exch hpt sub exch vpt add M + hpt2 vpt2 neg V currentpoint stroke M + hpt2 neg 0 R hpt2 vpt2 V stroke} def +/TriU {stroke [] 0 setdash 2 copy vpt 1.12 mul add M + hpt neg vpt -1.62 mul V + hpt 2 mul 0 V + hpt neg vpt 1.62 mul V closepath stroke + Pnt} def +/Star {2 copy Pls Crs} def +/BoxF {stroke [] 0 setdash exch hpt sub exch vpt add M + 0 vpt2 neg V hpt2 0 V 0 vpt2 V + hpt2 neg 0 V closepath fill} def +/TriUF {stroke [] 0 setdash vpt 1.12 mul add M + hpt neg vpt -1.62 mul V + hpt 2 mul 0 V + hpt neg vpt 1.62 mul V closepath fill} def +/TriD {stroke [] 0 setdash 2 copy vpt 1.12 mul sub M + hpt neg vpt 1.62 mul V + hpt 2 mul 0 V + hpt neg vpt -1.62 mul V closepath stroke + Pnt} def +/TriDF {stroke [] 0 setdash vpt 1.12 mul sub M + hpt neg vpt 1.62 mul V + hpt 2 mul 0 V + hpt neg vpt -1.62 mul V closepath fill} def +/DiaF {stroke [] 0 setdash vpt add M + hpt neg vpt neg V hpt vpt neg V + hpt vpt V hpt neg vpt V closepath fill} def +/Pent {stroke [] 0 setdash 2 copy gsave + translate 0 hpt M 4 {72 rotate 0 hpt L} repeat + closepath stroke grestore Pnt} def +/PentF {stroke [] 0 setdash gsave + translate 0 hpt M 4 {72 rotate 0 hpt L} repeat + closepath fill grestore} def +/Circle {stroke [] 0 setdash 2 copy + hpt 0 360 arc stroke Pnt} def +/CircleF {stroke [] 0 setdash hpt 0 360 arc fill} def +/C0 {BL [] 0 setdash 2 copy moveto vpt 90 450 arc} bind def +/C1 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 0 90 arc closepath fill + vpt 0 360 arc closepath} bind def +/C2 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 90 180 arc closepath fill + vpt 0 360 arc closepath} bind def +/C3 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 0 180 arc closepath fill + vpt 0 360 arc closepath} bind def +/C4 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 180 270 arc closepath fill + vpt 0 360 arc closepath} bind def +/C5 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 0 90 arc + 2 copy moveto + 2 copy vpt 180 270 arc closepath fill + vpt 0 360 arc} bind def +/C6 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 90 270 arc closepath fill + vpt 0 360 arc closepath} bind def +/C7 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 0 270 arc closepath fill + vpt 0 360 arc closepath} bind def +/C8 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 270 360 arc closepath fill + vpt 0 360 arc closepath} bind def +/C9 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 270 450 arc closepath fill + vpt 0 360 arc closepath} bind def +/C10 {BL [] 0 setdash 2 copy 2 copy moveto vpt 270 360 arc closepath fill + 2 copy moveto + 2 copy vpt 90 180 arc closepath fill + vpt 0 360 arc closepath} bind def +/C11 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 0 180 arc closepath fill + 2 copy moveto + 2 copy vpt 270 360 arc closepath fill + vpt 0 360 arc closepath} bind def +/C12 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 180 360 arc closepath fill + vpt 0 360 arc closepath} bind def +/C13 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 0 90 arc closepath fill + 2 copy moveto + 2 copy vpt 180 360 arc closepath fill + vpt 0 360 arc closepath} bind def +/C14 {BL [] 0 setdash 2 copy moveto + 2 copy vpt 90 360 arc closepath fill + vpt 0 360 arc} bind def +/C15 {BL [] 0 setdash 2 copy vpt 0 360 arc closepath fill + vpt 0 360 arc closepath} bind def +/Rec {newpath 4 2 roll moveto 1 index 0 rlineto 0 exch rlineto + neg 0 rlineto closepath} bind def +/Square {dup Rec} bind def +/Bsquare {vpt sub exch vpt sub exch vpt2 Square} bind def +/S0 {BL [] 0 setdash 2 copy moveto 0 vpt rlineto BL Bsquare} bind def +/S1 {BL [] 0 setdash 2 copy vpt Square fill Bsquare} bind def +/S2 {BL [] 0 setdash 2 copy exch vpt sub exch vpt Square fill Bsquare} bind def +/S3 {BL [] 0 setdash 2 copy exch vpt sub exch vpt2 vpt Rec fill Bsquare} bind def +/S4 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def +/S5 {BL [] 0 setdash 2 copy 2 copy vpt Square fill + exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def +/S6 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill Bsquare} bind def +/S7 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill + 2 copy vpt Square fill Bsquare} bind def +/S8 {BL [] 0 setdash 2 copy vpt sub vpt Square fill Bsquare} bind def +/S9 {BL [] 0 setdash 2 copy vpt sub vpt vpt2 Rec fill Bsquare} bind def +/S10 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt Square fill + Bsquare} bind def +/S11 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt2 vpt Rec fill + Bsquare} bind def +/S12 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill Bsquare} bind def +/S13 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill + 2 copy vpt Square fill Bsquare} bind def +/S14 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill + 2 copy exch vpt sub exch vpt Square fill Bsquare} bind def +/S15 {BL [] 0 setdash 2 copy Bsquare fill Bsquare} bind def +/D0 {gsave translate 45 rotate 0 0 S0 stroke grestore} bind def +/D1 {gsave translate 45 rotate 0 0 S1 stroke grestore} bind def +/D2 {gsave translate 45 rotate 0 0 S2 stroke grestore} bind def +/D3 {gsave translate 45 rotate 0 0 S3 stroke grestore} bind def +/D4 {gsave translate 45 rotate 0 0 S4 stroke grestore} bind def +/D5 {gsave translate 45 rotate 0 0 S5 stroke grestore} bind def +/D6 {gsave translate 45 rotate 0 0 S6 stroke grestore} bind def +/D7 {gsave translate 45 rotate 0 0 S7 stroke grestore} bind def +/D8 {gsave translate 45 rotate 0 0 S8 stroke grestore} bind def +/D9 {gsave translate 45 rotate 0 0 S9 stroke grestore} bind def +/D10 {gsave translate 45 rotate 0 0 S10 stroke grestore} bind def +/D11 {gsave translate 45 rotate 0 0 S11 stroke grestore} bind def +/D12 {gsave translate 45 rotate 0 0 S12 stroke grestore} bind def +/D13 {gsave translate 45 rotate 0 0 S13 stroke grestore} bind def +/D14 {gsave translate 45 rotate 0 0 S14 stroke grestore} bind def +/D15 {gsave translate 45 rotate 0 0 S15 stroke grestore} bind def +/DiaE {stroke [] 0 setdash vpt add M + hpt neg vpt neg V hpt vpt neg V + hpt vpt V hpt neg vpt V closepath stroke} def +/BoxE {stroke [] 0 setdash exch hpt sub exch vpt add M + 0 vpt2 neg V hpt2 0 V 0 vpt2 V + hpt2 neg 0 V closepath stroke} def +/TriUE {stroke [] 0 setdash vpt 1.12 mul add M + hpt neg vpt -1.62 mul V + hpt 2 mul 0 V + hpt neg vpt 1.62 mul V closepath stroke} def +/TriDE {stroke [] 0 setdash vpt 1.12 mul sub M + hpt neg vpt 1.62 mul V + hpt 2 mul 0 V + hpt neg vpt -1.62 mul V closepath stroke} def +/PentE {stroke [] 0 setdash gsave + translate 0 hpt M 4 {72 rotate 0 hpt L} repeat + closepath stroke grestore} def +/CircE {stroke [] 0 setdash + hpt 0 360 arc stroke} def +/Opaque {gsave closepath 1 setgray fill grestore 0 setgray closepath} def +/DiaW {stroke [] 0 setdash vpt add M + hpt neg vpt neg V hpt vpt neg V + hpt vpt V hpt neg vpt V Opaque stroke} def +/BoxW {stroke [] 0 setdash exch hpt sub exch vpt add M + 0 vpt2 neg V hpt2 0 V 0 vpt2 V + hpt2 neg 0 V Opaque stroke} def +/TriUW {stroke [] 0 setdash vpt 1.12 mul add M + hpt neg vpt -1.62 mul V + hpt 2 mul 0 V + hpt neg vpt 1.62 mul V Opaque stroke} def +/TriDW {stroke [] 0 setdash vpt 1.12 mul sub M + hpt neg vpt 1.62 mul V + hpt 2 mul 0 V + hpt neg vpt -1.62 mul V Opaque stroke} def +/PentW {stroke [] 0 setdash gsave + translate 0 hpt M 4 {72 rotate 0 hpt L} repeat + Opaque stroke grestore} def +/CircW {stroke [] 0 setdash + hpt 0 360 arc Opaque stroke} def +/BoxFill {gsave Rec 1 setgray fill grestore} def +/Density { + /Fillden exch def + currentrgbcolor + /ColB exch def /ColG exch def /ColR exch def + /ColR ColR Fillden mul Fillden sub 1 add def + /ColG ColG Fillden mul Fillden sub 1 add def + /ColB ColB Fillden mul Fillden sub 1 add def + ColR ColG ColB setrgbcolor} def +/BoxColFill {gsave Rec PolyFill} def +/PolyFill {gsave Density fill grestore grestore} def +/h {rlineto rlineto rlineto gsave closepath fill grestore} bind def +% +% PostScript Level 1 Pattern Fill routine for rectangles +% Usage: x y w h s a XX PatternFill +% x,y = lower left corner of box to be filled +% w,h = width and height of box +% a = angle in degrees between lines and x-axis +% XX = 0/1 for no/yes cross-hatch +% +/PatternFill {gsave /PFa [ 9 2 roll ] def + PFa 0 get PFa 2 get 2 div add PFa 1 get PFa 3 get 2 div add translate + PFa 2 get -2 div PFa 3 get -2 div PFa 2 get PFa 3 get Rec + gsave 1 setgray fill grestore clip + currentlinewidth 0.5 mul setlinewidth + /PFs PFa 2 get dup mul PFa 3 get dup mul add sqrt def + 0 0 M PFa 5 get rotate PFs -2 div dup translate + 0 1 PFs PFa 4 get div 1 add floor cvi + {PFa 4 get mul 0 M 0 PFs V} for + 0 PFa 6 get ne { + 0 1 PFs PFa 4 get div 1 add floor cvi + {PFa 4 get mul 0 2 1 roll M PFs 0 V} for + } if + stroke grestore} def +% +/languagelevel where + {pop languagelevel} {1} ifelse + 2 lt + {/InterpretLevel1 true def} + {/InterpretLevel1 Level1 def} + ifelse +% +% PostScript level 2 pattern fill definitions +% +/Level2PatternFill { +/Tile8x8 {/PaintType 2 /PatternType 1 /TilingType 1 /BBox [0 0 8 8] /XStep 8 /YStep 8} + bind def +/KeepColor {currentrgbcolor [/Pattern /DeviceRGB] setcolorspace} bind def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke} +>> matrix makepattern +/Pat1 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke + 0 4 M 4 8 L 8 4 L 4 0 L 0 4 L stroke} +>> matrix makepattern +/Pat2 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop 0 0 M 0 8 L + 8 8 L 8 0 L 0 0 L fill} +>> matrix makepattern +/Pat3 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop -4 8 M 8 -4 L + 0 12 M 12 0 L stroke} +>> matrix makepattern +/Pat4 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop -4 0 M 8 12 L + 0 -4 M 12 8 L stroke} +>> matrix makepattern +/Pat5 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop -2 8 M 4 -4 L + 0 12 M 8 -4 L 4 12 M 10 0 L stroke} +>> matrix makepattern +/Pat6 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop -2 0 M 4 12 L + 0 -4 M 8 12 L 4 -4 M 10 8 L stroke} +>> matrix makepattern +/Pat7 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop 8 -2 M -4 4 L + 12 0 M -4 8 L 12 4 M 0 10 L stroke} +>> matrix makepattern +/Pat8 exch def +<< Tile8x8 + /PaintProc {0.5 setlinewidth pop 0 -2 M 12 4 L + -4 0 M 12 8 L -4 4 M 8 10 L stroke} +>> matrix makepattern +/Pat9 exch def +/Pattern1 {PatternBgnd KeepColor Pat1 setpattern} bind def +/Pattern2 {PatternBgnd KeepColor Pat2 setpattern} bind def +/Pattern3 {PatternBgnd KeepColor Pat3 setpattern} bind def +/Pattern4 {PatternBgnd KeepColor Landscape {Pat5} {Pat4} ifelse setpattern} bind def +/Pattern5 {PatternBgnd KeepColor Landscape {Pat4} {Pat5} ifelse setpattern} bind def +/Pattern6 {PatternBgnd KeepColor Landscape {Pat9} {Pat6} ifelse setpattern} bind def +/Pattern7 {PatternBgnd KeepColor Landscape {Pat8} {Pat7} ifelse setpattern} bind def +} def +% +% +%End of PostScript Level 2 code +% +/PatternBgnd { + TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse +} def +% +% Substitute for Level 2 pattern fill codes with +% grayscale if Level 2 support is not selected. +% +/Level1PatternFill { +/Pattern1 {0.250 Density} bind def +/Pattern2 {0.500 Density} bind def +/Pattern3 {0.750 Density} bind def +/Pattern4 {0.125 Density} bind def +/Pattern5 {0.375 Density} bind def +/Pattern6 {0.625 Density} bind def +/Pattern7 {0.875 Density} bind def +} def +% +% Now test for support of Level 2 code +% +Level1 {Level1PatternFill} {Level2PatternFill} ifelse +% +/Symbol-Oblique /Symbol findfont [1 0 .167 1 0 0] makefont +dup length dict begin {1 index /FID eq {pop pop} {def} ifelse} forall +currentdict end definefont pop
--- a/CADDSuite/galaxyconfigs/tool_conf.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tool_conf.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <toolbox> - <label text="CADDSuite 0.94" id="cadds" /> + <label text="CADDSuite 0.95" id="cadds" /> <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> + <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"/>
--- a/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94"> +<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95"> <description>rescore w/ anti-target dock-results</description> <command interpreter="bash"><![CDATA[../../AntitargetRescorer #if str( $t ) != '' and str( $t ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="t" label="input file w/ target dock-results" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="at" label="input file w/ anti-target dock-results" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="t" optional="false" label="input file w/ target dock-results" type="data" format="mol2/sdf/drf"/> + <param name="at" optional="false" label="input file w/ anti-target dock-results" type="data" format="mol2/sdf/drf"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="t"/>
--- a/CADDSuite/galaxyconfigs/tools/AutoModel.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="automodel" name="AutoModel" version="1.1"> +<tool id="automodel" name="AutoModel" version="0.95"> <description>automatically find best QSAR model</description> <command interpreter="bash"><![CDATA[../../AutoModel #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input data-file" optional="false" type="data" format="dat"/> - <param name="min_quality" label="minimal desired quality (default: 0.3)" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/> + <param name="i" optional="false" label="input data-file" type="data" format="dat"/> + <param name="min_quality" optional="true" label="Optional: minimal desired quality (default: 0.3)" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/> </inputs> <outputs> <data name="o" format="mod"/>
--- a/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94"> +<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95"> <description>fix bindingdb.org downloads</description> <command interpreter="bash"><![CDATA[../../BindingDBCleaner #if str( $i ) != '' and str( $i ) != 'None' : @@ -18,12 +18,12 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="type" label="type of contained activity values: 'Ki' or 'IC50'" optional="false" type="select"> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="type" optional="false" label="type of contained activity values: 'Ki' or 'IC50'" type="select"> <option value="IC50">IC50</option> <option value="Ki">Ki</option> </param> - <param name="target" label="binding-DB target name" optional="false" area="true" type="text" size="1x15"/> + <param name="target" optional="false" label="binding-DB target name" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94"> +<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95"> <description>generate combinatorial lib</description> <command interpreter="bash"><![CDATA[../../CombiLibGenerator #if str( $i ) != '' and str( $i ) != 'None' : @@ -12,7 +12,7 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/> + <param name="i" optional="false" label="input combi-lib file" type="data" format="data"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf"/> @@ -23,7 +23,6 @@ <scaffold> Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3 - Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3 <moietyR1> [R1]C(C)(C)C <moietyR2>
--- a/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94"> +<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95"> <description>find strongly interacting residues</description> <command interpreter="bash"><![CDATA[../../ConstraintsFinder #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -18,9 +18,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> </inputs> <outputs> <data name="o" format="ini"/>
--- a/CADDSuite/galaxyconfigs/tools/Converter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Converter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="converter" name="Converter" version="0.94"> +<tool id="converter" name="Converter" version="0.95"> <description>interconvert molecular file-formats</description> <command interpreter="bash"><![CDATA[../../Converter #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="f" label="output format" optional="true" type="select"> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="f" optional="true" label="output format" type="select"> <option value="mol2">mol2</option> <option value="sdf">sdf</option> <option value="drf">drf</option>
--- a/CADDSuite/galaxyconfigs/tools/DBExporter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="dbexporter" name="DBExporter" version="0.94 (ob)"> +<tool id="dbexporter" name="DBExporter" version="0.95 (ob)"> <description>export molecules from data base</description> <command interpreter="bash"><![CDATA[../../DBExporter #if str( $o ) != '' and str( $o ) != 'None' : @@ -69,26 +69,26 @@ | tail -n 5 ]]></command> <inputs> - <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/> - <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> - <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> - <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> - <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/> - <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> - <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> - <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> - <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/> - <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> - <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> - <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> - <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> - <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> - <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/> + <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="data"/> + <param name="start_id" optional="true" label="Optional: ID of the first conformation to be exported" type="text" area="true" size="1x5" value=""/> + <param name="end_id" optional="true" label="Optional: ID of the last conformation to be exported" type="text" area="true" size="1x5" value=""/> + <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> + <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> + <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/> + <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/> + <param name="max_mols" optional="true" label="Optional: max. number of molecules to be exported" type="text" area="true" size="1x5" value=""/> + <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/> + <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/> + <param name="uck" optional="true" label="Optional: UCK key" area="true" type="text" size="1x15"/> + <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/> + <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/> + <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/> + <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/> + <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/> + <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf"/>
--- a/CADDSuite/galaxyconfigs/tools/DBImporter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="dbimporter" name="DBImporter" version="0.94 (ob)"> +<tool id="dbimporter" name="DBImporter" version="0.95 (ob)"> <description>import molecules into data base</description> <command interpreter="bash"><![CDATA[../../DBImporter #if str( $i ) != '' and str( $i ) != 'None' : @@ -39,17 +39,17 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/> - <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> - <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> - <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> - <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> - <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> - <param name="vn" label="name of compound vendor" optional="true" area="true" type="text" size="1x15"/> - <param name="vid" label="name of vendor's compound-ID tag in sd-file" optional="true" area="true" type="text" size="1x15"/> - <param name="vd" label="vendor library date or version" optional="true" area="true" type="text" size="1x15"/> - <param name="vu" label="url from wich vendor library was obtained" optional="true" area="true" type="text" size="1x15"/> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/> + <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/> + <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/> + <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/> + <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/> + <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/> + <param name="vn" optional="true" label="Optional: name of compound vendor" area="true" type="text" size="1x15"/> + <param name="vid" optional="true" label="Optional: name of vendor's compound-ID tag in sd-file" area="true" type="text" size="1x15"/> + <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/> + <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/> </inputs> <outputs/> <help>This tool imports molecules into a database.
--- a/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="dockresultmerger" name="DockResultMerger" version="0.94"> +<tool id="dockresultmerger" name="DockResultMerger" version="0.95"> <description>merge docking output files</description> <command interpreter="bash"><![CDATA[../../DockResultMerger #for $s in $series_i @@ -30,13 +30,13 @@ ]]></command> <inputs> <repeat name="series_i" title="input files" min="1"> - <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="i" optional="false" label="input files" type="data" format="mol2/sdf/drf"/> </repeat> - <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/> - <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="score" optional="true" label="Optional: score property name" area="true" type="text" size="1x15" value="score"/> + <param name="min" optional="true" label="Optional: minimal score value" type="text" area="true" size="1x5" value=""/> + <param name="max" optional="true" label="Optional: maximal score value" type="text" area="true" size="1x5" value=""/> + <param name="k" optional="true" label="Optional: number of output molecules" type="text" area="true" size="1x5" value=""/> + <param name="rm" optional="true" label="remove input files after merging" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="evensplit" name="EvenSplit" version="0.94"> +<tool id="evensplit" name="EvenSplit" version="0.95"> <description>generate splits w/ equal property range</description> <command interpreter="bash"><![CDATA[../../EvenSplit #if str( $i ) != '' and str( $i ) != 'None' : @@ -12,26 +12,26 @@ #if str( $o2 ) != '' and str( $o2 ) != 'None' : -o2 "$o2" #end if +#if str( $prop ) != '' and str( $prop ) != 'None' : + -prop "$prop" +#end if #if str( $n ) != '' and str( $n ) != 'None' : -n "$n" #end if -#if str( $offset ) != '' and str( $offset ) != 'None' : - -offset "$offset" -#end if #if str( $k ) != '' and str( $k ) != 'None' : -k "$k" #end if -#if str( $prop ) != '' and str( $prop ) != 'None' : - -prop "$prop" +#if str( $offset ) != '' and str( $offset ) != 'None' : + -offset "$offset" #end if | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="n" label="number of compounds to use from input file" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="offset" label="extract each (i+offset)%k == 0 for o2" optional="true" type="text" area="true" size="1x5" value="0"/> - <param name="k" label="extract each k'th compound for 2nd output file" optional="true" type="text" area="true" size="1x5" value="2"/> - <param name="prop" label="property name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="prop" optional="false" label="property name" area="true" type="text" size="1x15" value="binding_free_energy"/> + <param name="n" optional="true" label="Optional: max. number of compounds to use from input file" type="text" area="true" size="1x5" value=""/> + <param name="k" optional="true" label="Optional: extract each k'th compound to 2nd output file" type="text" area="true" size="1x5" value="2"/> + <param name="offset" optional="true" label="Optional: offset; extract each (i+offset)%k == 0 to 2nd output file" type="text" area="true" size="1x5" value="0"/> </inputs> <outputs> <data name="o1" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="featureselector" name="FeatureSelector" version="1.1"> +<tool id="featureselector" name="FeatureSelector" version="0.95"> <description>run feature-selection on a QSAR model</description> <command interpreter="bash"><![CDATA[../../FeatureSelector #if str( $i ) != '' and str( $i ) != 'None' : @@ -18,9 +18,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input mod-file" optional="false" type="data" format="mod"/> - <param name="dat" label="data-file" optional="false" type="data" format="dat"/> - <param name="type" label="feature-selection type" optional="false" type="select"> + <param name="i" optional="false" label="input mod-file" type="data" format="mod"/> + <param name="dat" optional="false" label="data-file" type="data" format="dat"/> + <param name="type" optional="false" label="feature-selection type" type="select"> <option value="remove_correlated">remove_correlated</option> <option value="forward_selection">forward_selection</option> <option value="backward_selection">backward_selection</option>
--- a/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94"> +<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95"> <description>generate galaxy tool-config files</description> <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator #if str( $i ) != '' and str( $i ) != 'None' : @@ -18,8 +18,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input par-file" optional="false" type="data" format="data"/> - <param name="ignore" label="tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" optional="true" area="true" size="1x5"/> + <param name="i" optional="false" label="input par-file" type="data" format="data"/> + <param name="ignore" optional="true" label="Optional: tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" area="true" size="1x5"/> </inputs> <outputs> <data name="o" format="xml"/>
--- a/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="gridbuilder" name="GridBuilder" version="0.94"> +<tool id="gridbuilder" name="GridBuilder" version="0.95"> <description>create score-grids for docking</description> <command interpreter="bash"><![CDATA[../../GridBuilder #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -18,9 +18,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> </inputs> <outputs> <data name="grd" format="grd.tgz"/>
--- a/CADDSuite/galaxyconfigs/tools/IMGDock.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="imeedydock" name="IMGDock" version="0.94"> +<tool id="imeedydock" name="IMGDock" version="0.95"> <description>Iterative Multi-Greedy Docking</description> <command interpreter="bash"><![CDATA[../../IMGDock #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -24,11 +24,11 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> - <param name="i" label="compounds to be docked" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="grd" label="ScoreGrid file" optional="false" type="data" format="grd.tgz"/> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> + <param name="i" optional="false" label="compounds to be docked" type="data" format="mol2/sdf/drf"/> + <param name="grd" optional="false" label="ScoreGrid file" type="data" format="grd.tgz"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="inputpartitioner" name="InputPartitioner" version="1.1"> +<tool id="inputpartitioner" name="InputPartitioner" version="0.95"> <description>split QSAR data set</description> <command interpreter="bash"><![CDATA[../../InputPartitioner #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input data-file" optional="false" type="data" format="dat"/> - <param name="n" label="number of partitions" optional="false" type="text" area="true" size="1x5" value=""/> + <param name="i" optional="false" label="input data-file" type="data" format="dat"/> + <param name="n" optional="false" label="number of partitions" type="text" area="true" size="1x5" value=""/> </inputs> <outputs> <data name="o" format="dat"/>
--- a/CADDSuite/galaxyconfigs/tools/InputReader.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="inputreader" name="InputReader" version="1.1"> +<tool id="inputreader" name="InputReader" version="0.95"> <description>generate QSAR data set</description> <command interpreter="bash"><![CDATA[../../InputReader #if str( $i ) != '' and str( $i ) != 'None' : @@ -39,16 +39,16 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/> - <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/> - <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/> - <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/> + <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/> + <param name="act" optional="true" label="Optional: sd-property containing response values" area="true" type="text" size="1x15"/> + <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/> + <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/> + <param name="sdp" optional="true" label="use sd-properties as additional descriptors" type="boolean" truevalue="true" falsevalue=""/> + <param name="no_cd" optional="true" label="do not center descriptors" type="boolean" truevalue="true" falsevalue=""/> + <param name="no_cr" optional="true" label="do not center response values" type="boolean" truevalue="true" falsevalue=""/> + <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/> + <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="dat"/>
--- a/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94"> +<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95"> <description>define interaction constraint</description> <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner #if str( $res ) != '' and str( $res ) != 'None' : @@ -21,10 +21,10 @@ | tail -n 5 ]]></command> <inputs> - <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/> - <param name="res" label="residue ID" optional="false" area="true" type="text" size="1x15"/> - <param name="s" label="desired minimal interation (score) between ligand and specified residue(s)" optional="false" type="text" area="true" size="1x5" value="-2.0"/> - <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="10"/> + <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/> + <param name="res" optional="false" label="residue ID" area="true" type="text" size="1x15"/> + <param name="s" optional="false" label="desired minimal interation (score) between ligand and specified residue(s)" type="text" area="true" size="1x5" value="-2.0"/> + <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="10"/> </inputs> <outputs> <data name="o" format="ini"/>
--- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="ligcheck" name="LigCheck" version="0.94"> +<tool id="ligcheck" name="LigCheck" version="0.95"> <description>check molecules for errors</description> <command interpreter="bash"><![CDATA[../../LigCheck #if str( $i ) != '' and str( $i ) != 'None' : @@ -21,10 +21,10 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/> - <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> + <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/> + <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/> + <param name="ut" optional="true" label="check for unique topologies (default: check only for unique conformation)" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94"> +<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95"> <description>generate 3D coordinates for small molecules</description> <command interpreter="bash"><![CDATA[../../Ligand3DGenerator #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94"> +<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95"> <description>split molecule files</description> <command interpreter="bash"><![CDATA[../../LigandFileSplitter #if str( $i ) != '' and str( $i ) != 'None' : @@ -57,8 +57,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="no" label="no. of splits to be created" optional="false" type="hidden" area="true" size="1x5" value="15"/> + <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> + <param name="no" optional="false" label="no. of splits to be created" type="hidden" area="true" size="1x5" value="15"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/ModelCreator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -18,8 +18,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input dat-file" optional="false" type="data" format="dat"/> - <param name="type" label="model type" optional="false" type="select"> + <param name="i" optional="false" label="input dat-file" type="data" format="dat"/> + <param name="type" optional="false" label="model type" type="select"> <option value="MLR">MLR</option> <option value="RR">RR</option> <option value="PCR">PCR</option> @@ -34,7 +34,7 @@ <option value="snB">snB</option> <option value="nB">nB</option> </param> - <param name="kernel" label="kernel type (in case of kernel-model)" optional="true" type="select"> + <param name="kernel" optional="true" label="kernel type (in case of kernel-model)" type="select"> <option value="none">none</option> <option value="polynomial">polynomial</option> <option value="rbf">rbf</option>
--- a/CADDSuite/galaxyconfigs/tools/MolCombine.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="molcombine" name="MolCombine" version="0.94"> +<tool id="molcombine" name="MolCombine" version="0.95"> <description>combine molecular files</description> <command interpreter="bash"><![CDATA[../../MolCombine #if str( $i1 ) != '' and str( $i1 ) != 'None' : @@ -24,15 +24,15 @@ | tail -n 5 ]]></command> <inputs> - <param name="i1" label="input molecule file A" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="i2" label="input molecule file B" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="mode" label="'intersection', 'union' or 'b_not_a'" optional="false" type="select"> + <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/> + <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/> + <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select"> <option value="intersection">intersection</option> <option value="union">union</option> <option value="b_not_a">b_not_a</option> </param> - <param name="ignH" label="ignore hydrogens, i.e. match molecules to any protonation state." optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="replace_prop" label="replace properties from file 1 w/ those from file 2" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/> + <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i1"/>
--- a/CADDSuite/galaxyconfigs/tools/MolDepict.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="moldepict" name="MolDepict" version="0.94"> +<tool id="moldepict" name="MolDepict" version="0.95"> <description>create structure diagrams</description> <command interpreter="bash"><![CDATA[../../MolDepict #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="max" label="maximal number of pictures (default=60, 0=unlimited)" optional="true" type="text" area="true" size="1x5" value="60"/> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="max" optional="true" label="Optional: maximal number of pictures (default=60, 0=unlimited)" type="text" area="true" size="1x5" value="60"/> </inputs> <outputs> <data name="o" format="pdf"/>
--- a/CADDSuite/galaxyconfigs/tools/MolFilter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -40,16 +40,16 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/> - <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> - <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> + <param name="i" optional="false" label="input molecule-file" type="data" format="mol2/sdf/drf"/> + <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="txt"/> + <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="data"/> + <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" area="true" size="1x5" value=""/> + <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" area="true" size="1x5" value=""/> + <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/> + <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/> + <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" area="true" size="1x5" value=""/> + <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" area="true" size="1x5" value=""/> + <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="molpredictor" name="MolPredictor" version="1.1"> +<tool id="molpredictor" name="MolPredictor" version="0.95"> <description>predict molecule activities with QSAR model</description> <command interpreter="bash"><![CDATA[../../MolPredictor #if str( $i ) != '' and str( $i ) != 'None' : @@ -30,13 +30,13 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/> - <param name="mod" label="file containing QSAR model" optional="false" type="data" format="mod"/> - <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/> - <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> - <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> - <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/> + <param name="mod" optional="false" label="file containing QSAR model" type="data" format="mod"/> + <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/> + <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/> + <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/> + <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/> + <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="sdf"/>
--- a/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="pdbcutter" name="PDBCutter" version="0.94"> +<tool id="pdbcutter" name="PDBCutter" version="0.95"> <description>separate ligand and receptor</description> <command interpreter="bash"><![CDATA[../../PDBCutter #if str( $i ) != '' and str( $i ) != 'None' : @@ -27,11 +27,11 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/> - <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/> - <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/> - <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/> - <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/> + <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/> + <param name="lig_chain" optional="false" label="chain-name of ligand" area="true" type="text" size="1x15"/> + <param name="lig_name" optional="false" label="ligand name" area="true" type="text" size="1x15"/> + <param name="rm_ch" optional="true" label="Optional: protein chains that are to be deleted" area="true" type="text" size="1x15"/> + <param name="rm_res" optional="true" label="Optional: pdb-residues that are to be deleted (e.g. water or ions)" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="rec" format="pdb"/>
--- a/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="pdbdownload" name="PDBDownload" version="0.94"> +<tool id="pdbdownload" name="PDBDownload" version="0.95"> <description>retrieve pdb-file from pdb.org</description> <command interpreter="bash"><![CDATA[../../PDBDownload #if str( $id ) != '' and str( $id ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="id" label="PDB ID for desired structure" optional="false" area="true" type="text" size="1x15"/> - <param name="p" label="proxy" optional="true" area="true" type="text" size="1x15"/> + <param name="id" optional="false" label="PDB ID for desired structure" area="true" type="text" size="1x15"/> + <param name="p" optional="true" label="Optional: proxy" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="pdb"/>
--- a/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94"> +<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95"> <description>transfer part. charges between files</description> <command interpreter="bash"><![CDATA[../../PartialChargesCopy #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="chr" label="file containing the same molecules as the input file, but with (different) partial charges" optional="false" type="data" format="mol2"/> + <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> + <param name="chr" optional="false" label="file containing the same molecules as the input file, but with (different) partial charges" type="data" format="mol2"/> </inputs> <outputs> <data name="o" format="mol2" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="pocketdetector" name="PocketDetector" version="0.94"> +<tool id="pocketdetector" name="PocketDetector" version="0.95"> <description>detect binding pocket</description> <command interpreter="bash"><![CDATA[../../PocketDetector #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -18,9 +18,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="input ini file" optional="true" type="data" format="ini"/> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="input ini file" type="data" format="ini"/> </inputs> <outputs> <data name="o" format="ini"/>
--- a/CADDSuite/galaxyconfigs/tools/Predictor.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="predictor" name="Predictor" version="1.1"> +<tool id="predictor" name="Predictor" version="0.95"> <description>predict activities with QSAR model</description> <command interpreter="bash"><![CDATA[../../Predictor #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input mod-file" optional="false" type="data" format="mod"/> - <param name="dat" label="data-file containing prediction data set" optional="false" type="data" format="dat"/> + <param name="i" optional="false" label="input mod-file" type="data" format="mod"/> + <param name="dat" optional="false" label="data-file containing prediction data set" type="data" format="dat"/> </inputs> <outputs> <data name="o" format="txt"/>
--- a/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="propertymodifier" name="PropertyModifier" version="0.94"> +<tool id="propertymodifier" name="PropertyModifier" version="0.95"> <description>modify molecule property tags</description> <command interpreter="bash"><![CDATA[../../PropertyModifier #if str( $i ) != '' and str( $i ) != 'None' : @@ -24,15 +24,15 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="mode" label="'delete', 'add' or 'rename' properties" optional="false" type="select"> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="mode" optional="false" label="'delete', 'add' or 'rename' properties" type="select"> <option value="add">add</option> <option value="rename">rename</option> <option value="delete">delete</option> </param> - <param name="name" label="property name ('all' will erase all properties if in delete-mode)" optional="false" area="true" type="text" size="1x15"/> - <param name="value" label="property value (in case of prop. adding only)" optional="true" area="true" type="text" size="1x15"/> - <param name="new_name" label="new property name (in case of renaming only)" optional="true" area="true" type="text" size="1x15"/> + <param name="name" optional="false" label="property name ('all' will erase all properties if in delete-mode)" area="true" type="text" size="1x15"/> + <param name="value" optional="true" label="Optional: property value (in case of prop. adding only)" area="true" type="text" size="1x15"/> + <param name="new_name" optional="true" label="Optional: new property name (in case of renaming only)" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="propertyplotter" name="PropertyPlotter" version="0.94"> +<tool id="propertyplotter" name="PropertyPlotter" version="0.95"> <description>plot molecule properties</description> <command interpreter="bash"><![CDATA[../../PropertyPlotter #if str( $i ) != '' and str( $i ) != 'None' : @@ -19,9 +19,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="p1" label="name of property 1" optional="false" area="true" type="text" size="1x15"/> - <param name="p2" label="name of property 2" optional="true" area="true" type="text" size="1x15"/> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="p1" optional="false" label="name of property 1" area="true" type="text" size="1x15"/> + <param name="p2" optional="true" label="Optional: name of property 2" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="png"/>
--- a/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="proteincheck" name="ProteinCheck" version="0.94"> +<tool id="proteincheck" name="ProteinCheck" version="0.95"> <description>quality check for proteins structures</description> <command interpreter="bash"><![CDATA[../../ProteinCheck #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/> - <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/> + <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="pdf"/>
--- a/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="proteinprotonator" name="ProteinProtonator" version="0.94"> +<tool id="proteinprotonator" name="ProteinProtonator" version="0.95"> <description>protonate protein structures</description> <command interpreter="bash"><![CDATA[../../ProteinProtonator #if str( $i ) != '' and str( $i ) != 'None' : @@ -15,8 +15,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="pdb"/> - <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/> + <param name="i" optional="false" label="input file" type="data" format="pdb"/> + <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> </inputs> <outputs> <data name="o" format="pdb" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94"> +<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95"> <description>calculate RMSD between poses</description> <command interpreter="bash"><![CDATA[../../RMSDCalculator #if str( $i ) != '' and str( $i ) != 'None' : @@ -16,8 +16,8 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> + <param name="org" optional="false" label="molecule file containing the original ('true') poses" type="data" format="mol2/sdf/drf"/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94"> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95"> <description>generate ROC or enrichment plots</description> <command interpreter="bash"><![CDATA[../../ScoreAnalyzer #if str( $mode ) != '' and str( $mode ) != 'None' : @@ -30,18 +30,18 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select"> + <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> + <param name="mode" optional="false" label="'roc', 'top50', 'scatter' or 'enrichment'" type="select"> <option value="roc">roc</option> <option value="top50">top50</option> <option value="scatter">scatter</option> <option value="enrichment">enrichment</option> </param> - <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/> - <param name="s" label="score label" optional="false" area="true" type="text" size="1x15" value="score"/> - <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> - <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/> - <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/> + <param name="s" optional="false" label="score label" area="true" type="text" size="1x15" value="score"/> + <param name="e" optional="false" label="binding-free-energy/class label name" area="true" type="text" size="1x15" value="binding_free_energy"/> + <param name="t" optional="true" label="Optional: only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" area="true" type="text" size="1x15"/> + <param name="b" optional="true" label="binary experimental activity data" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="png"/>
--- a/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml Tue Jul 12 10:23:33 2011 -0400 @@ -19,9 +19,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="i1" label="input molecule file 1" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="i2" label="input molecule file 2" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/> + <param name="i1" optional="false" label="input molecule file 1" type="data" format="mol2/sdf/drf"/> + <param name="i2" optional="false" label="input molecule file 2" type="data" format="mol2/sdf/drf"/> + <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/> </inputs> <outputs> <data name="o" format="png"/>
--- a/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="simplerescorer" name="SimpleRescorer" version="0.94"> +<tool id="simplerescorer" name="SimpleRescorer" version="0.95"> <description>rescore docking results</description> <command interpreter="bash"><![CDATA[../../SimpleRescorer #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -24,11 +24,11 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> - <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="function" label="scoring function: 'MM', 'PLP' or 'PB'" optional="true" type="select"> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> + <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> + <param name="function" optional="true" label="scoring function: 'MM', 'PLP' or 'PB'" type="select"> <option value="MM">MM</option> <option value="PLP">PLP</option> <option value="PB">PB</option>
--- a/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94"> +<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95"> <description>define spatial constraint</description> <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner #if str( $ini ) != '' and str( $ini ) != 'None' : @@ -24,14 +24,14 @@ | tail -n 5 ]]></command> <inputs> - <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/> - <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="type" label="'fraction' or 'number' of compound atoms" optional="false" type="select"> + <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/> + <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> + <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select"> <option value="fraction">fraction</option> <option value="number">number</option> </param> - <param name="n" label="desired number/fraction of atoms in spatial area" optional="false" type="text" area="true" size="1x5" value=""/> - <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="1e11"/> + <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/> + <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="1e11"/> </inputs> <outputs> <data name="o" format="ini"/>
--- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="tagres-train" name="TaGRes-train" version="0.94"> +<tool id="tagres-train" name="TaGRes-train" version="0.95"> <description>Target-specific Grid-Rescoring, training</description> <command interpreter="bash"><![CDATA[../../TaGRes-train #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -30,20 +30,20 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> - <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> + <param name="i" optional="false" label="training compound data set" type="data" format="mol2/sdf/drf"/> + <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select"> <option value="Rescoring3D">Rescoring3D</option> <option value="Rescoring4D">Rescoring4D</option> <option value="Rescoring1D">Rescoring1D</option> </param> - <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> + <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select"> <option value="MM">MM</option> <option value="PLP">PLP</option> </param> - <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> + <param name="exp" optional="false" label="property-tag name containing experimentally determined binding-free-energies" area="true" type="text" size="1x15" value="binding_free_energy"/> </inputs> <outputs> <data name="o" format="mod"/> @@ -55,7 +55,7 @@ * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein. -A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it. +A scoring function is applied and an interaction-grid is thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it. -The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help> +The output of TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help> </tool> \ No newline at end of file
--- a/CADDSuite/galaxyconfigs/tools/TaGRes.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="tagres" name="TaGRes" version="0.94"> +<tool id="tagres" name="TaGRes" version="0.95"> <description>Target-specific Grid-Rescoring</description> <command interpreter="bash"><![CDATA[../../TaGRes #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -18,6 +18,9 @@ #if str( $mod ) != '' and str( $mod ) != 'None' : -mod "$mod" #end if +#if str( $tf ) != '' and str( $tf ) != 'None' : + -tf "$tf" +#end if #if str( $o ) != '' and str( $o ) != 'None' : -o "$o" #end if @@ -30,17 +33,18 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> - <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/> - <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> + <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> + <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="data"/> + <param name="tf" optional="true" label="Optional: top-scored fraction of compounds not to be rescored" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select"> <option value="Rescoring3D">Rescoring3D</option> <option value="Rescoring4D">Rescoring4D</option> <option value="Rescoring1D">Rescoring1D</option> </param> - <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> + <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select"> <option value="MM">MM</option> <option value="PLP">PLP</option> </param>
--- a/CADDSuite/galaxyconfigs/tools/Validator.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Validator.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="validator" name="Validator" version="1.1"> +<tool id="validator" name="Validator" version="0.95"> <description>evaluate quality of a QSAR model</description> <command interpreter="bash"><![CDATA[../../Validator #if str( $i ) != '' and str( $i ) != 'None' : @@ -18,9 +18,9 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input mod-file" optional="false" type="data" format="mod"/> - <param name="dat" label="data-file" optional="false" type="data" format="dat"/> - <param name="type" label="feature-selection type" optional="false" type="select"> + <param name="i" optional="false" label="input mod-file" type="data" format="mod"/> + <param name="dat" optional="false" label="data-file" type="data" format="dat"/> + <param name="type" optional="false" label="feature-selection type" type="select"> <option value="cross validation">cross validation</option> <option value="bootstrapping">bootstrapping</option> <option value="response permutation">response permutation</option>
--- a/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="vendorfinder" name="VendorFinder" version="0.94"> +<tool id="vendorfinder" name="VendorFinder" version="0.95"> <description>search vendors for compounds</description> <command interpreter="bash"><![CDATA[../../VendorFinder #if str( $i ) != '' and str( $i ) != 'None' : @@ -30,13 +30,13 @@ | tail -n 5 ]]></command> <inputs> - <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> - <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> - <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> - <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> - <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> - <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="i" optional="false" label="input file containing compounds" type="data" format="mol2/sdf/drf"/> + <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/> + <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/> + <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/> + <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/> + <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/> + <param name="opt" optional="true" label="optimize purchase, i.e. select cheapest sources and sort by vendor" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="txt"/>
--- a/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="waterfinder" name="WaterFinder" version="0.94"> +<tool id="waterfinder" name="WaterFinder" version="0.95"> <description>find strongly bound waters</description> <command interpreter="bash"><![CDATA[../../WaterFinder #if str( $rec ) != '' and str( $rec ) != 'None' : @@ -24,11 +24,11 @@ | tail -n 5 ]]></command> <inputs> - <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> - <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> - <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> - <param name="wat" label="input pdb-file containing water molecules (if not part of rec.-file)" optional="true" type="data" format="pdb"/> - <param name="ai" label="use ab-initio water search (ignore water in pdb-file), experimental!" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> + <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> + <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> + <param name="wat" optional="true" label="input pdb-file containing water molecules (if not part of rec.-file)" type="data" format="pdb"/> + <param name="ai" optional="true" label="use ab-initio water search (ignore water in pdb-file), experimental!" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="pdb"/>
--- a/CADDSuite/rescoring_common Tue Jun 28 10:37:20 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/rescoring_common.bin "$@"
--- a/CADDSuite/setPathes.sh Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/setPathes.sh Tue Jul 12 10:23:33 2011 -0400 @@ -5,6 +5,7 @@ export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/ export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/ export PATH="$BASE_DIR"/bin:$PATH -export GDFONTPATH="$BASE_DIR"/data/fonts +export GDFONTPATH="$BASE_DIR"/data/gnuplot export GNUPLOT_DEFAULT_GDFONT=FreeSans +export GNUPLOT_PS_DIR="$BASE_DIR"/data/gnuplot
--- a/CADDSuite/suite_config.xml Tue Jun 28 10:37:20 2011 -0400 +++ b/CADDSuite/suite_config.xml Tue Jul 12 10:23:33 2011 -0400 @@ -1,4 +1,4 @@ -<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.94"> +<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.95"> <description> CADDSuite: A flexible and open framework for Computer-Aided Drug Design @@ -6,135 +6,135 @@ <tool id="cadds_upload" name="Upload File" version="1.1.2"> <description>from your computer</description> </tool> -<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94"> +<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95"> <description>rescore w/ anti-target dock-results</description> </tool> -<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94"> +<tool id="automodel" name="AutoModel" version="0.95"> + <description>automatically find best QSAR model</description> +</tool> +<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95"> <description>fix bindingdb.org downloads</description> </tool> -<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94"> +<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95"> <description>generate combinatorial lib</description> </tool> -<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94"> +<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95"> <description>find strongly interacting residues</description> </tool> -<tool id="converter" name="Converter" version="0.94"> +<tool id="converter" name="Converter" version="0.95"> <description>interconvert molecular file-formats</description> </tool> -<tool id="dbexporter" name="DBExporter" version="0.94 (ob)"> +<tool id="dbexporter" name="DBExporter" version="0.95 (ob)"> <description>export molecules from data base</description> </tool> -<tool id="dbimporter" name="DBImporter" version="0.94 (ob)"> +<tool id="dbimporter" name="DBImporter" version="0.95 (ob)"> <description>import molecules into data base</description> </tool> -<tool id="dockresultmerger" name="DockResultMerger" version="0.94"> +<tool id="dockresultmerger" name="DockResultMerger" version="0.95"> <description>merge docking output files</description> </tool> -<tool id="evensplit" name="EvenSplit" version="0.94"> +<tool id="evensplit" name="EvenSplit" version="0.95"> <description>generate splits w/ equal property range</description> </tool> -<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94"> +<tool id="featureselector" name="FeatureSelector" version="0.95"> + <description>run feature-selection on a QSAR model</description> +</tool> +<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95"> <description>generate galaxy tool-config files</description> </tool> -<tool id="gridbuilder" name="GridBuilder" version="0.94"> +<tool id="gridbuilder" name="GridBuilder" version="0.95"> <description>create score-grids for docking</description> </tool> -<tool id="imeedydock" name="IMGDock" version="0.94"> +<tool id="imeedydock" name="IMGDock" version="0.95"> <description>Iterative Multi-Greedy Docking</description> </tool> -<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94"> +<tool id="inputpartitioner" name="InputPartitioner" version="0.95"> + <description>split QSAR data set</description> +</tool> +<tool id="inputreader" name="InputReader" version="0.95"> + <description>generate QSAR data set</description> +</tool> +<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95"> <description>define interaction constraint</description> </tool> -<tool id="ligcheck" name="LigCheck" version="0.94"> +<tool id="ligcheck" name="LigCheck" version="0.95"> <description>check molecules for errors</description> </tool> -<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94"> +<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95"> <description>generate 3D coordinates for small molecules</description> </tool> -<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94"> +<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95"> <description>split molecule files</description> </tool> -<tool id="molcombine" name="MolCombine" version="0.94"> +<tool id="modelcreator" name="ModelCreator" version="1.1"> + <description>create a QSAR model</description> +</tool> +<tool id="molcombine" name="MolCombine" version="0.95"> <description>combine molecular files</description> </tool> -<tool id="moldepict" name="MolDepict" version="0.94"> +<tool id="moldepict" name="MolDepict" version="0.95"> <description>create structure diagrams</description> </tool> <tool id="molfilter" name="MolFilter" version="0.9"> <description>filter molecule files</description> </tool> -<tool id="pdbcutter" name="PDBCutter" version="0.94"> +<tool id="molpredictor" name="MolPredictor" version="0.95"> + <description>predict molecule activities with QSAR model</description> +</tool> +<tool id="pdbcutter" name="PDBCutter" version="0.95"> <description>separate ligand and receptor</description> </tool> -<tool id="pdbdownload" name="PDBDownload" version="0.94"> +<tool id="pdbdownload" name="PDBDownload" version="0.95"> <description>retrieve pdb-file from pdb.org</description> </tool> -<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94"> +<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95"> <description>transfer part. charges between files</description> </tool> -<tool id="pocketdetector" name="PocketDetector" version="0.94"> +<tool id="pocketdetector" name="PocketDetector" version="0.95"> <description>detect binding pocket</description> </tool> -<tool id="propertymodifier" name="PropertyModifier" version="0.94"> +<tool id="predictor" name="Predictor" version="0.95"> + <description>predict activities with QSAR model</description> +</tool> +<tool id="propertymodifier" name="PropertyModifier" version="0.95"> <description>modify molecule property tags</description> </tool> -<tool id="propertyplotter" name="PropertyPlotter" version="0.94"> +<tool id="propertyplotter" name="PropertyPlotter" version="0.95"> <description>plot molecule properties</description> </tool> -<tool id="proteincheck" name="ProteinCheck" version="0.94"> +<tool id="proteincheck" name="ProteinCheck" version="0.95"> <description>quality check for proteins structures</description> </tool> -<tool id="proteinprotonator" name="ProteinProtonator" version="0.94"> +<tool id="proteinprotonator" name="ProteinProtonator" version="0.95"> <description>protonate protein structures</description> </tool> -<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94"> +<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95"> <description>calculate RMSD between poses</description> </tool> -<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94"> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95"> <description>generate ROC or enrichment plots</description> </tool> <tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9"> <description>analyze similarity between molecule files</description> </tool> -<tool id="simplerescorer" name="SimpleRescorer" version="0.94"> +<tool id="simplerescorer" name="SimpleRescorer" version="0.95"> <description>rescore docking results</description> </tool> -<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94"> +<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95"> <description>define spatial constraint</description> </tool> -<tool id="tagres-train" name="TaGRes-train" version="0.94"> +<tool id="tagres-train" name="TaGRes-train" version="0.95"> <description>Target-specific Grid-Rescoring, training</description> </tool> -<tool id="tagres" name="TaGRes" version="0.94"> +<tool id="tagres" name="TaGRes" version="0.95"> <description>Target-specific Grid-Rescoring</description> </tool> -<tool id="vendorfinder" name="VendorFinder" version="0.94"> +<tool id="validator" name="Validator" version="0.95"> + <description>evaluate quality of a QSAR model</description> +</tool> +<tool id="vendorfinder" name="VendorFinder" version="0.95"> <description>search vendors for compounds</description> </tool> -<tool id="waterfinder" name="WaterFinder" version="0.94"> +<tool id="waterfinder" name="WaterFinder" version="0.95"> <description>find strongly bound waters</description> -</tool> -<tool id="automodel" name="AutoModel" version="1.1"> - <description>automatically find best QSAR model</description> -</tool> -<tool id="featureselector" name="FeatureSelector" version="1.1"> - <description>run feature-selection on a QSAR model</description> -</tool> -<tool id="inputpartitioner" name="InputPartitioner" version="1.1"> - <description>split QSAR data set</description> -</tool> -<tool id="inputreader" name="InputReader" version="1.1"> - <description>generate QSAR data set</description> -</tool> -<tool id="modelcreator" name="ModelCreator" version="1.1"> - <description>create a QSAR model</description> -</tool> -<tool id="molpredictor" name="MolPredictor" version="1.1"> - <description>predict molecule activities with QSAR model</description> -</tool> -<tool id="predictor" name="Predictor" version="1.1"> - <description>predict activities with QSAR model</description> -</tool> -<tool id="validator" name="Validator" version="1.1"> - <description>evaluate quality of a QSAR model</description> </tool></suite>