# HG changeset patch # User luis # Date 1468341213 14400 # Node ID 605370bc1defa8fb0d27a02c4d7fcd93a138e584 # Parent 31013b5cd0669cc95be3ce2c6ed273fe7028f25e Uploaded diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/AddMissingAtoms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/AddMissingAtoms.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,39 @@ + + + + + add missing atoms to protein structures + + AddMissingAtoms + macros.xml + + + + AddMissingAtoms + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_opt_hyd: + -opt_hyd $param_opt_hyd +#end if + + + + + + + + + + AddMissingAtoms tool allows you to missing atoms, i.e. hydrogens to a protein structure. + + Optional parameter is the optimize_hydrogens flag (-opt_hyd), which uses the AMBER force field to run a quick energy minization for all hydrogen atoms. + +Output of this tool is one pdb-file containing the input protein structure with added atoms. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/AntitargetRescorer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/AntitargetRescorer.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,42 @@ + + + + + rescore w/ anti-target dock-results + + AntitargetRescorer + macros.xml + + + + AntitargetRescorer + +#if $param_t: + -t $param_t +#end if +#if $param_at: + -at $param_at +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + + This tool rescores docking output poses. +AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file. + +As input we need: + * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target). + * a file containing the same compounds docked into the antitarget. + +Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/AutoModel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/AutoModel.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,37 @@ + + + + + automatically find best QSAR model + + AutoModel + macros.xml + + + + AutoModel + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_min_quality: + -min_quality $param_min_quality +#end if + + + + + + + + + + This tool tries to automatically find the best QSAR model for a given data set. + +It therefore applies nested validation, including feature selection, for each available model-type. The model with the best nested prediction quality is saved to the specified output file. However, if the best obtained nested prediction quality is smaller than the value specified by '-min_quality', an error will be shown and no model will be saved. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/BindingDBCleaner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/BindingDBCleaner.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,58 @@ + + + + + fix bindingdb.org downloads + + BindingDBCleaner + macros.xml + + + + BindingDBCleaner + +#if $param_i: + -i $param_i +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_o: + -o $param_o +#end if +#if $param_target: + -target "$param_target" +#end if + + + + + + + + + + + + + + + + + + + + + This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org. + +For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'. + +All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/BondOrderAssigner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/BondOrderAssigner.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,86 @@ + + + + + computes bond order assignments for a ligand + + BondOrderAssigner + macros.xml + + + + BondOrderAssigner + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_max_sol: + -max_sol $param_max_sol +#end if +#if $param_scr_pen: + -scr_pen + #if " " in str($param_scr_pen): + "$param_scr_pen" + #else + $param_scr_pen + #end if +#end if +#if $param_non_opt: + -non_opt $param_non_opt +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_id: + -o_id "$adv_opts.param_o_id" +#end if + #if $adv_opts.param_o_dir: + -o_dir "$adv_opts.param_o_dir" +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool computes optimal and sub-optimal bond order assignments based on an atomic penalty function for a given ligand in mol2 file format. + +Optional parameters are the maximal number of solutions to be computed ('-max_sol'), the penalty table specifiying the atomic penalty rules ('-scr_pen'),and a flag indicating if sub-optimal solutions should be computed as well ('-non_opt'). + +Output of this tool is a number of mol2 files each containing one bond order assignment. + +To upload an input file please use the upload tool (Get Data -> Upload File). + +**Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help. + +Please cite the following: Dehof, A.K., Rurainski, A., Bui, Q.B.A., Boecker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011 + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/CalculateBindingFreeEnergy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/CalculateBindingFreeEnergy.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,32 @@ + + + + + calculate binding energy of two proteins using AMBER + + CalculateBindingFreeEnergy + macros.xml + + + + CalculateBindingFreeEnergy + +#if $param_pdb_a: + -pdb_a $param_pdb_a +#end if +#if $param_pdb_b: + -pdb_b $param_pdb_b +#end if + + + + + + + + + + This tool computes the binding energy of two given pdb files using the AMBER force field. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/CalculateEnergy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/CalculateEnergy.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,64 @@ + + + + + calculate free energy of a protein + + CalculateEnergy + macros.xml + + + + CalculateEnergy + +#if $param_pdb: + -pdb $param_pdb +#end if +#if $param_force_field: + -force_field + #if " " in str($param_force_field): + "$param_force_field" + #else + $param_force_field + #end if +#end if +#if $param_non_bond_cutoff: + -non_bond_cutoff $param_non_bond_cutoff +#end if +#if $param_elec_stat_cuton: + -elec_stat_cuton $param_elec_stat_cuton +#end if +#if $param_elec_stat_cutoff: + -elec_stat_cutoff $param_elec_stat_cutoff +#end if +#if $param_dist_dep_dielec: + -dist_dep_dielec $param_dist_dep_dielec +#end if +#if $param_overwrite_types: + -overwrite_types $param_overwrite_types +#end if +#if $param_overwrite_charges: + -overwrite_charges $param_overwrite_charges +#end if + + + + + + + + + + + + + + + + + + + This tool computes the free energy of a pdb file using a specified force field (-force_field) and force field parameters (-non_bond_cutoff, -elec_stat_cuton ... ). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/CalculateSolvationFreeEnergy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/CalculateSolvationFreeEnergy.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,36 @@ + + + + + calculate solvation free energy of a protein using AMBER + + CalculateSolvationFreeEnergy + macros.xml + + + + CalculateSolvationFreeEnergy + +#if $param_pdb: + -pdb $param_pdb +#end if +#if $param_epsilon_medium: + -epsilon_medium $param_epsilon_medium +#end if +#if $param_epsilon_vacuum: + -epsilon_vacuum $param_epsilon_vacuum +#end if + + + + + + + + + + + This tool computes the solvation free energy of a pdb file using the Jackson-Sternberg approach (bonded energy using a force field and a non bonded energy (electrostatics only) by solving the Poisson-Boltzmann equation. Parameters are the dielectric constants for the medium (-epsilon_medium) and the vacuum (-epsilon_vacuum). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/CombiLibGenerator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/CombiLibGenerator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,42 @@ + + + + + generate combinatorial lib + + CombiLibGenerator + macros.xml + + + + CombiLibGenerator + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties. + +As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need: + +<scaffold> + Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3 +<moietyR1> + [R1]C(C)(C)C +<moietyR2> + [R2]OC(C)(C)C + +Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ConstraintsFinder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ConstraintsFinder.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,99 @@ + + + + + find strongly interacting residues + + ConstraintsFinder + macros.xml + + + + ConstraintsFinder + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_option: + -option $param_option +#end if +#if $param_o: + -o $param_o +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + This tool searches protein residues with which the reference ligand interacts strongly. +Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion. + +As input we need: + * a file containing a protonated protein in pdb-format + * 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). + +Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/Converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/Converter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,96 @@ + + + + + interconvert molecular file-formats + + Converter + macros.xml + + + + Converter + +#if $param_i: + -i $param_i +#end if +#if $param_if: + -if + #if " " in str($param_if): + "$param_if" + #else + $param_if + #end if +#end if +#if $param_o: + -o $param_o +#end if +#if $param_of: + -of + #if " " in str($param_of): + "$param_of" + #else + $param_of + #end if +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool can be used to convert between different molecular file-formats. +Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz. File extensions of input and output filenames are ignored. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/CrystalGenerator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/CrystalGenerator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,324 @@ + + + + + creates crystals + + CrystalGenerator + macros.xml + + + + CrystalGenerator + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_sg: + -sg + #if " " in str($param_sg): + "$param_sg" + #else + $param_sg + #end if +#end if +#if $param_axis_a: + -axis_a $param_axis_a +#end if +#if $param_axis_b: + -axis_b $param_axis_b +#end if +#if $param_axis_c: + -axis_c $param_axis_c +#end if +#if $param_angle_alpha: + -angle_alpha $param_angle_alpha +#end if +#if $param_angle_beta: + -angle_beta $param_angle_beta +#end if +#if $param_angle_gamma: + -angle_gamma $param_angle_gamma +#end if +#if $param_from_uc_a: + -from_uc_a $param_from_uc_a +#end if +#if $param_from_uc_b: + -from_uc_b $param_from_uc_b +#end if +#if $param_from_uc_c: + -from_uc_c $param_from_uc_c +#end if +#if $param_to_uc_a: + -to_uc_a $param_to_uc_a +#end if +#if $param_to_uc_b: + -to_uc_b $param_to_uc_b +#end if +#if $param_to_uc_c: + -to_uc_c $param_to_uc_c +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + TODO: Manual + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/DockPoseClustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/DockPoseClustering.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,178 @@ + + + + + clusters docking poses + + DockPoseClustering + macros.xml + + + + DockPoseClustering + +#if $param_i_pdb: + -i_pdb $param_i_pdb +#end if +#if $param_i_dcd: + -i_dcd $param_i_dcd +#end if +#if $param_i_trans: + -i_trans $param_i_trans +#end if +#if $param_o_index_list: + -o_index_list $param_o_index_list +#end if +#if $param_o_score_matrix: + -o_score_matrix $param_o_score_matrix +#end if +#if $param_o_dcd: + -o_dcd $param_o_dcd +#end if +#if $param_rmsd_cutoff: + -rmsd_cutoff $param_rmsd_cutoff +#end if +#if $param_alg: + -alg + #if " " in str($param_alg): + "$param_alg" + #else + $param_alg + #end if +#end if +#if $param_scope: + -scope + #if " " in str($param_scope): + "$param_scope" + #else + $param_scope + #end if +#end if +#if $param_rmsd_type: + -rmsd_type + #if " " in str($param_rmsd_type): + "$param_rmsd_type" + #else + $param_rmsd_type + #end if +#end if +#if $param_o_red_dcd: + -o_red_dcd $param_o_red_dcd +#end if +#if $param_o_cluster_tree: + -o_cluster_tree $param_o_cluster_tree +#end if +#if $param_refine_alg: + -refine_alg + #if " " in str($param_refine_alg): + "$param_refine_alg" + #else + $param_refine_alg + #end if +#end if +#if $param_refine_rmsd_type: + -refine_rmsd_type + #if " " in str($param_refine_rmsd_type): + "$param_refine_rmsd_type" + #else + $param_refine_rmsd_type + #end if +#end if +#if $param_refine_rmsd_scope: + -refine_rmsd_scope + #if " " in str($param_refine_rmsd_scope): + "$param_refine_rmsd_scope" + #else + $param_refine_rmsd_scope + #end if +#end if +#if $param_use_refinement: + -use_refinement $param_use_refinement +#end if +#if $param_run_serial: + -run_serial $param_run_serial +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_dcd_id: + -o_dcd_id "$adv_opts.param_o_dcd_id" +#end if + #if $adv_opts.param_o_dcd_dir: + -o_dcd_dir "$adv_opts.param_o_dcd_dir" +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool computes clusters of docking poses given as conformation set or a list of rigid transformations. + +Parameters are either the input ConformationSet (-i_dcd) and one corresponding pdb file (-i_pdb), or a transformation file (-i_trans). Output can be a cluster index list (-o_index_list), a cluster scoring matrix (-o_score_matrix), or dcd files per cluster (-o_dcd). Optional parameters are the algorithm (-alg), the minimal rmsd between the final clusters (-rmsd_cutoff), the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope). The optional parameter -o_red_dcd sets the output file for the reduced cluster set (one representative per cluster). The optional parameter -o_cluster_tree specifies the output file for storing the cluster tree. + +Output of this tool depends in the choice of the output parameters. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/DockResultMerger.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/DockResultMerger.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,62 @@ + + + + + merge docking output files + + DockResultMerger + macros.xml + + + + DockResultMerger + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_score: + -score "$param_score" +#end if +#if $param_min: + -min $param_min +#end if +#if $param_max: + -max $param_max +#end if +#if $param_k: + -k $param_k +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + + + + + + + + This tool merges and sorts molecule files as generated by docking or rescoring. + +You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file. + + Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/EvenSplit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/EvenSplit.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,58 @@ + + + + + generate splits w/ equal property range + + EvenSplit + macros.xml + + + + EvenSplit + +#if $param_i: + -i $param_i +#end if +#if $param_o1: + -o1 $param_o1 +#end if +#if $param_o2: + -o2 $param_o2 +#end if +#if $param_prop: + -prop "$param_prop" +#end if +#if $param_n: + -n $param_n +#end if +#if $param_k: + -k $param_k +#end if +#if $param_offset: + -offset $param_offset +#end if + + + + + + + + + + + + + + + + + + + + + This tool splits a molecule file into two subsets in such a way that each of them convers an equal range of a property. The property with respect to which this is to be done should be specified with '-prop'. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ExtractClustersFromWardTree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ExtractClustersFromWardTree.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,79 @@ + + + + + extracts docking clusters + + ExtractClustersFromWardTree + macros.xml + + + + ExtractClustersFromWardTree + +#if $param_i: + -i $param_i +#end if +#if $param_i_type: + -i_type "$param_i_type" +#end if +#if $param_o_out: + -o_out $param_o_out +#end if +#if $param_o_type: + -o_type + #if " " in str($param_o_type): + "$param_o_type" + #else + $param_o_type + #end if +#end if +#if $param_cutoff_type: + -cutoff_type + #if " " in str($param_cutoff_type): + "$param_cutoff_type" + #else + $param_cutoff_type + #end if +#end if +#if $param_cut_value: + -cut_value $param_cut_value +#end if +#if $param_min_size: + -min_size $param_min_size +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool extracts clusters of docking poses given a dat file. + +Parameters are the filename (-i) of the serialized cluster tree, the output filename (-o_out), the output type (-o_type). The optional parameter -i_type allows to switch between binary (default) and text file for the cluster tree input, parameter -min_size allows to filter for cluster of a minimal size, parameter -cutoff_type defines the way to cut the cluster tree (either by ward distance or by a target number of clusters) using paramter -cut_value. + +Output of this tool is the extracted cluster tree, either as index list, as graph visualization (gv) input, or as json + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ExtractProteinChains.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ExtractProteinChains.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,67 @@ + + + + + separate all chains of a pdb file into separate pdb files + + ExtractProteinChains + macros.xml + + + + ExtractProteinChains + +#if $param_pdb: + -pdb $param_pdb +#end if +#if $param_chain_id: + -chain_id "$param_chain_id" +#end if +#if $param_o: + -o $param_o +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_id: + -o_id "$adv_opts.param_o_id" +#end if + #if $adv_opts.param_o_dir: + -o_dir "$adv_opts.param_o_dir" +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool splits a pdb file into its chains. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ExtractProteinSequence.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ExtractProteinSequence.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,42 @@ + + + + + extracts fasta sequence + + ExtractProteinSequence + macros.xml + + + + ExtractProteinSequence + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_c: + -c "$param_c" +#end if + + + + + + + + + + + + + + + + + This tool extracts the fasta sequence from a given pdb file. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/FeatureSelector.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/FeatureSelector.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,56 @@ + + + + + run feature-selection on a QSAR model + + FeatureSelector + macros.xml + + + + FeatureSelector + +#if $param_i: + -i $param_i +#end if +#if $param_dat: + -dat $param_dat +#end if +#if $param_o: + -o $param_o +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if + + + + + + + + + + + + + + + + + + FeatureSelector runs a feature-selection for a given QSAR model. + +The type of feature-selection to be done is specified by '-type'. Input of this tool is a data file as generated by InputReader containing the training data for feature-selection and a QSAR model file as generated by ModelCreator (or this tool itself). Note that you can apply several feature-selection methods in succession by using the output of one call of this tool as input for the next call. +Model- and kernel-parameters (if any) will be automatically optimized by cross-validation after applying the desired feature-selection. + +Output of this tool is a model-file that can be used by other QuEasy tools (e.g. Validator). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/FingerprintSimilarityClustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/FingerprintSimilarityClustering.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,117 @@ + + + + + fast clustering of compounds using 2D binary fingerprints + + FingerprintSimilarityClustering + macros.xml + + + + FingerprintSimilarityClustering + +#if $param_t: + -t $param_t +#end if +#if $param_f: + -f $param_f +#end if +#if $param_fp_col: + -fp_col $param_fp_col +#end if +#if $param_id_col: + -id_col $param_id_col +#end if +#if $param_fp_tag: + -fp_tag "$param_fp_tag" +#end if +#if $param_id_tag: + -id_tag "$param_id_tag" +#end if +#if $param_tc: + -tc $param_tc +#end if +#if $param_cc: + -cc $param_cc +#end if +#if $param_l: + -l $param_l +#end if +#if $param_nt: + -nt "$param_nt" +#end if +#if $param_sdf_out: + -sdf_out $param_sdf_out +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool performs a fast and deterministic semi-hierarchical clustering of input compounds encoded as 2D binary fingerprints. + +The method is a multistep workflow which first reduces the number of input fingerprints by removing duplicates. This unique set is forwarded to connected +components decomposition by calculating all pairwise Tanimoto similarities and application of a similarity cutoff value. As a third step, all connected components +which exceed a predefined size are hierarchically clustered using the average linkage clustering criterion. The Kelley method is applied on every hierarchical clustering +to determine a level for cluster selection. Finally, the fingerprint duplicates are remapped onto the final clusters which contain their representatives. + +For every final cluster a medoid is calulated. For a single cluster multiple medoids are possible because fingerprint duplicates of a medoid are also marked as medoid. + +For every compound the output yields a cluster ID, a medoid tag where '1' indicates the cluster medoid(s) and the average similarity of the compound to all other +cluster members. If the output format is SD, these properties are added as new tags. + +====================================================================================================================================================== + +Examples: + +$ FingerprintSimilarityClustering -t target.sdf -fp_tag FPRINT -f 1 -id_tag NAME + tries to read fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf input file. + The clustering workflow described is executed on the input molecules with default values. + +$ FingerprintSimilarityClustering -t target.csv -fp_col 3 -f 2 -id_col 1 + tries to read fingerprints as comma separated integer feature list (-f 2) from column 3 and IDs from column 1 out of a space separated CSV file. + The clustering workflow described is executed on the input molecules with default values. + +$ FingerprintSimilarityClustering -t target.sdf -fp_tag FPRINT -f 1 -id_tag NAME -nt max + Same as first example but executed in parallel mode using as many threads as available. + +$ FingerprintSimilarityClustering -t target.sdf -fp_tag FPRINT -f 1 -id_tag NAME -tc 0.5 -cc 50 + Same as first example but using modified parameters for similarity network generation (tc 0.5) and size of connected components to be clustered (-cc 50). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/FingerprintSimilaritySearch.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/FingerprintSimilaritySearch.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,114 @@ + + + + + calculate similar molecules in a library + + FingerprintSimilaritySearch + macros.xml + + + + FingerprintSimilaritySearch + +#if $param_t: + -t $param_t +#end if +#if $param_q: + -q $param_q +#end if +#if $param_o: + -o $param_o +#end if +#if $param_f: + -f $param_f +#end if +#if $param_fp_col: + -fp_col $param_fp_col +#end if +#if $param_id_col: + -id_col $param_id_col +#end if +#if $param_fp_tag: + -fp_tag "$param_fp_tag" +#end if +#if $param_id_tag: + -id_tag "$param_id_tag" +#end if +#if $param_tc: + -tc $param_tc +#end if +#if $param_nt: + -nt "$param_nt" +#end if +#if $param_bs: + -bs $param_bs +#end if +#if $param_sdf_out: + -sdf_out $param_sdf_out +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool calculates all nearest neighbours above a similarity cutoff for given query molecules in a compound library on the basis of 2D binary fingerprints. +The first library to specify (i1) is the compound library to be searched, the second library (i2) is conseiderd as the query compounds. +Both files have to be comma separated values (csv) files and the binary fingerprints have to be encoded as feature lists or as binary bit strings. + +WARNING: If similarity cutoff is chosen to be 0.0, the output will be the entire similarity matrix and has a size of n*m with n=|i1| and m=|i2|. + +====================================================================================================================================================== + +Examples: + +$ FingerprintSimilaritySearch -t target.sdf -q query.sdf -o results -fp_tag FPRINT -f 1 -id_tag NAME + tries to extract fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf and query.sdf. + A similarity search is performed for all query molecules against all target molecules and pairs with similarity above Tanimoto cutoff 0.7 are written to outfile (results). + +$ FingerprintSimilaritySearch -t target.sdf -q query.sdf -o results -fp_tag FPRINT -f 1 -id_tag NAME -sdf_out + tries to extract fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf and query.sdf. + A similarity search is performed for all query molecules against all target molecules and pairs with similarity above Tanimoto cutoff 0.7 + are added as a new SD tag to output file 'NN_TAGGED_query.sdf' as a list of TargetID:Similarity pairs. + +$ FingerprintSimilaritySearch -t target.sdf -q query.smi -o results -fp_tag FPRINT -f 1 -id_tag NAME -fp_col 2 + tries to extract fingerprints as binary bitstrings (-f 1) from tag <FPRINT> and compound IDs from tag <NAME> of target.sdf + and fingerprints as binary bitstrings of space separated query file from column 2 (-fp_col 2). + A similarity search is performed for all query molecules against all target molecules and pairs with similarity above Tanimoto cutoff 0.7 are written to outfile (results). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/GridBuilder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/GridBuilder.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,110 @@ + + + + + create score-grids for docking + + GridBuilder + macros.xml + + + + GridBuilder + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_grd: + -grd $param_grd +#end if +#if $param_pocket: + -pocket $param_pocket +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_atom_types: + -ScoringFunction:atom_types "$adv_opts.param_ScoringFunction_atom_types" +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool precalculates a score-grid for a binding pocket of a given receptor. + +As input we need: + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. + This reference ligand should be located in the binding pocket, + so that a grid can be precalculated around it. + Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + +Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/IMGDock.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/IMGDock.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,148 @@ + + + + + Iterative Multi-Greedy Docking + + IMGDock + macros.xml + + + + IMGDock + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_pocket: + -pocket $param_pocket +#end if +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_grd: + -grd $param_grd +#end if +#if $param_rm: + -rm $param_rm +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_IMGDock_superpose_ligand: + -IMGDock:superpose_ligand +#end if + #if $adv_opts.param_IMGDock_decrease_stepwidth: + -IMGDock:decrease_stepwidth +#end if + #if $adv_opts.param_IMGDock_output_failed_dockings: + -IMGDock:output_failed_dockings +#end if + #if $adv_opts.param_IMGDock_iterations: + -IMGDock:iterations $adv_opts.param_IMGDock_iterations +#end if + #if $adv_opts.param_IMGDock_min_inhibitor_atoms: + -IMGDock:min_inhibitor_atoms $adv_opts.param_IMGDock_min_inhibitor_atoms +#end if + #if $adv_opts.param_IMGDock_post_optimization_step_width: + -IMGDock:post_optimization_step_width $adv_opts.param_IMGDock_post_optimization_step_width +#end if + #if $adv_opts.param_IMGDock_no_solutions: + -IMGDock:no_solutions $adv_opts.param_IMGDock_no_solutions +#end if + #if $adv_opts.param_IMGDock_post_optimization_steps: + -IMGDock:post_optimization_steps $adv_opts.param_IMGDock_post_optimization_steps +#end if + #if $adv_opts.param_IMGDock_step_width: + -IMGDock:step_width $adv_opts.param_IMGDock_step_width +#end if + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach. +As input we need: + + * a file containing a protonated protein in pdb-format + * 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 score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here. + * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck. + +Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound. + +Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/InputPartitioner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/InputPartitioner.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,38 @@ + + + + + split QSAR data set + + InputPartitioner + macros.xml + + + + InputPartitioner + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_n: + -n $param_n +#end if + + + + + + + + + + InputPartitioner partitions a given QSAR data set into n partitions with evenly distributed response values. +Thus, this tool can be useful as part of a nested validation pipeline. +Input is a data file as generated by InputReader. +Output will be written to n files postfixed '_TRAIN<i>.dat' and '_TEST<i>.dat', where <i> is the ID of the resp. partition. For each of these partitions, the training set contains only those compounds that were not selected for the resp. test set. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/InputReader.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/InputReader.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,85 @@ + + + + + generate QSAR data set + + InputReader + macros.xml + + + + InputReader + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_act: + -act "$param_act" +#end if +#if $param_csv: + -csv $param_csv +#end if +#if $param_csv_nr: + -csv_nr $param_csv_nr +#end if +#if $param_csv_sep: + -csv_sep $param_csv_sep +#end if +#if $param_sdp: + -sdp $param_sdp +#end if +#if $param_no_cd: + -no_cd $param_no_cd +#end if +#if $param_no_cr: + -no_cr $param_no_cr +#end if +#if $param_csv_cl: + -csv_cl $param_csv_cl +#end if +#if $param_csv_dl: + -csv_dl $param_csv_dl +#end if + + + + + + + + + + + + + + + + + + + + + + + + + This tool reads input from sd-files and generate features for QSAR analysis. +Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'. +The following number of features will be automatically created for each molecule in your sd-file: + + * 40 atom and bond count descriptors + * 2 connectivity indices (Balaban and Zagreb index) + * 4 partial charge descriptors + * 14 surface descriptors + * 133 topological descriptors (functional group counts) + +If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options. +Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/InteractionConstraintDefiner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/InteractionConstraintDefiner.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,54 @@ + + + + + define interaction constraint + + InteractionConstraintDefiner + macros.xml + + + + InteractionConstraintDefiner + +#if $param_res: + -res "$param_res" +#end if +#if $param_s: + -s $param_s +#end if +#if $param_p: + -p $param_p +#end if +#if $param_o: + -o $param_o +#end if +#if $param_option: + -option $param_option +#end if + + + + + + + + + + + + + + + + + + + This tool allows to define interaction constraints for docking or scoring. + +The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: <chain-ID>:<residue-ID>, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17. + +Output of this tool is a ini-file that contains the desired interaction constraint. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/LigCheck.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/LigCheck.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,63 @@ + + + + + check molecules for errors + + LigCheck + macros.xml + + + + LigCheck + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_ef: + -ef $param_ef +#end if +#if $param_ri: + -ri $param_ri +#end if +#if $param_ut: + -ut $param_ut +#end if +#if $param_nc: + -nc $param_nc +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + +The following checks are done for each molecule: + + * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem) + * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. + * each atom must have a valid assigned element + * the molecule must be protonated (since this is necessary for docking/(re-)scoring). + * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring) + * partial charges may not contain completely senseless values (>5 or <-5). + * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies. + +If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/Ligand3DGenerator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/Ligand3DGenerator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,70 @@ + + + + + generate 3D coordinates for small molecules + + Ligand3DGenerator + macros.xml + + + + Ligand3DGenerator + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_ph: + -ph $param_ph +#end if +#if $param_ff: + -ff "$param_ff" +#end if +#if $param_rm: + -rm $param_rm +#end if +#if $param_k: + -k $param_k +#end if +#if $param_kp: + -kp $param_kp +#end if + + + + + + + + + + + + + + + + + + + + + This tool takes input molecules and generates a single 3D conformation which is ready for docking. The input has to be a chemical file +containing valid topologies and conistent bond order assignements. 2D coordinates in the input file are overwritten, 3D coordinates can be kept ('-k' or '-kp'). + + '-k': 3D coordinates are tried to be kept. Molecules with non-zero coordinates in all three dimensions are passed through without modifications. + However, if a molecule is not ready for docking (i.e. unusual bond leghts, unusual charges), the molecule will be rebuild and new + 3D coordinates are assigned. If only hydrogens are missing, the coordinates of non-hydrogen atoms are kept but the molecule gets newly protonated. + '-kp': 3D coordinates are tried to be kept as for the '-k' flag but the molecule will be newly protonated. + +Please note that the main purpose of this tool is to generate valid starting conformations for docking or other optimization procedures. +Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) +different fragments might still overlap with each other. + +Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/LigandFileSplitter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/LigandFileSplitter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,91 @@ + + + + + split molecule files + + LigandFileSplitter + macros.xml + + + + LigandFileSplitter + +#if $param_i: + -i $param_i +#end if +#if $param_no: + -no $param_no +#end if +#if $param_mpf: + -mpf $param_mpf +#end if +#if $param_outname_pattern: + -outname_pattern "$param_outname_pattern" +#end if + +#if $rep_param_o: +-o + #for token in $rep_param_o: + #if " " in str(token): + "$token.param_o" + #else + $token.param_o + #end if + #end for +#end if + + + + + + + + + + + + + + + + + + + LigandFileSplitter splits a molecule file into a given number of subsets. + +Examples: + +$ LigandFileSplitter -i Trypsin_actives.sdf -o batch_1 batch_2 + will split the input file Trypsin_actives.sdf in the two output files batch_1.sdf and batch_2.sdf. + +$ LigandFileSplitter -i Trypsin_actives.sdf -no 3 + will split the input file Trypsin_actives.sdf in three files named Trypsin_actives_0.sdf, Trypsin_actives_1.sdf and Trypsin_actives_2.sdf + +$ LigandFileSplitter -i ligands.sdf -ligands_per_file 4 + will split the input file ligands.sdf in as many files needed to fit at most 4 ligands per file. + The files will be named ligands_0.sdf, ligands_1.sdf ... ligands_N.sdf + +$ LigandFileSplitter -i ligands.sdf -ligands_per_file 5 -outname_pattern split_ligands-%d.sdf + will split the input file ligands.sdf in as many files needed to fit at most 5 ligands per file. + The files will be named split_ligands-0.sdf, split_ligands-1.sdf, ... , split_ligands-N.sdf. + +$ LigandFileSplitter -i ligands.sdf -outname_pattern split_ligands_%d.sdf -no 100 + will split the input file ligands.sdf in 100 files using the following names: + split_ligands_0.sdf, split_ligands_1.sdf, ... , split_ligands_99.sdf. + +NOTES: +- Molecules are not sorted in any way. +- The tool is no format converter and the format of the output files will be the same as of the input file. +- Output_name_pattern accepts a printf-like pattern, expecting exactly one decimal integer placeholder, %d. +- The following are valid patterns: output_ligand.sdf_%d, split_%d.mol, %d_lig.drf +- The following are invalid patterns: output_%f.sdf, ligands.drf_%u, %d_lig_%d.mol, molecules.sdf + +WARNING: +- If the parameter outname_pattern is specified, the user is responsible for the occurrence of a valid file extension + in the outname_pattern, which has to be of the same file format as the input file. + + + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ModelCreator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ModelCreator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,73 @@ + + + + + create a QSAR model + + ModelCreator + macros.xml + + + + ModelCreator + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_kernel: + -kernel + #if " " in str($param_kernel): + "$param_kernel" + #else + $param_kernel + #end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ModelCreator creates a QSAR model using an input data set as generated by InputReader. + +The type of QSAR model to be used can be specified by '-type', the type of kernel-function (if any) can be chosen by '-kernel'. Optimization of model- and kernel-parmeters will be done automatically using cross-validation. + +Output of this tool is a model-file that can be used by other QuEasy tools (e.g. FeatureSelector). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/MolCombine.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/MolCombine.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,64 @@ + + + + + combine molecular files + + MolCombine + macros.xml + + + + MolCombine + +#if $param_i1: + -i1 $param_i1 +#end if +#if $param_i2: + -i2 $param_i2 +#end if +#if $param_mode: + -mode + #if " " in str($param_mode): + "$param_mode" + #else + $param_mode + #end if +#end if +#if $param_o: + -o $param_o +#end if +#if $param_ignH: + -ignH $param_ignH +#end if +#if $param_replace_prop: + -replace_prop $param_replace_prop +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + + + + + This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged. + +If you want to match molecules regardless of their protonation state, use option '-ignH'. + +Output of this tool is a file containing the union resp. intersection of all molecules of input A and B. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/MolDepict.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/MolDepict.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,38 @@ + + + + + create structure diagrams + + MolDepict + macros.xml + + + + MolDepict + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_max: + -max $param_max +#end if + + + + + + + + + + This tool create structure diagrams for small molecules. +Supported input-formats are mol, mol2, sdf, drf. + +Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/MolFilter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/MolFilter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,84 @@ + + + + + filter molecule files + + MolFilter + macros.xml + + + + MolFilter + +#if $param_i: + -i $param_i +#end if +#if $param_min_logP: + -min_logP $param_min_logP +#end if +#if $param_max_logP: + -max_logP $param_max_logP +#end if +#if $param_min_MW: + -min_MW $param_min_MW +#end if +#if $param_max_MW: + -max_MW $param_max_MW +#end if +#if $param_q: + -q $param_q +#end if +#if $param_min_sim: + -min_sim $param_min_sim +#end if +#if $param_max_sim: + -max_sim $param_max_sim +#end if +#if $param_smarts: + -smarts "$param_smarts" +#end if +#if $param_smarts_file: + -smarts_file $param_smarts_file +#end if +#if $param_o: + -o $param_o +#end if +#if $param_quiet: + -quiet $param_quiet +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s). + +Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/MolPredictor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/MolPredictor.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,68 @@ + + + + + predict molecule activities with QSAR model + + MolPredictor + macros.xml + + + + MolPredictor + +#if $param_i: + -i $param_i +#end if +#if $param_mod: + -mod $param_mod +#end if +#if $param_o: + -o $param_o +#end if +#if $param_csv: + -csv $param_csv +#end if +#if $param_csv_nr: + -csv_nr $param_csv_nr +#end if +#if $param_csv_sep: + -csv_sep $param_csv_sep +#end if +#if $param_sdp: + -sdp $param_sdp +#end if +#if $param_csv_cl: + -csv_cl $param_csv_cl +#end if +#if $param_csv_dl: + -csv_dl $param_csv_dl +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + + + + This tool predictes the response values of compounds in the given molecule file using the specified QSAR model. + +Input of this tool is a molecule file (sdf,mol2,drf) and a model-file as generated by ModelCreator or FeatureSelector. +Features for all molecules in the input file are generated automatically. However, if you used an additional, externally generated feature-set to generate your QSAR model, make sure to generate features in the same manner (i.e. using the same external tool with the same settings) for the molecule file to be used here and specify the csv-file with the above options. + +Output of this tool (as specified by '-o') is a molecule file containing the predicted values as a property tag named 'predicted_activity'. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PDBCutter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PDBCutter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,104 @@ + + + + + separate ligand and receptor + + PDBCutter + macros.xml + + + + PDBCutter + +#if $param_i: + -i $param_i +#end if +#if $param_rec: + -rec $param_rec +#end if +#if $param_lig: + -lig $param_lig +#end if +#if $param_lig_chain: + -lig_chain "$param_lig_chain" +#end if +#if $param_lig_name: + -lig_name "$param_lig_name" +#end if + +#if $rep_param_rm_ch: +-rm_ch + #for token in $rep_param_rm_ch: + #if " " in str(token): + "$token.param_rm_ch" + #else + $token.param_rm_ch + #end if + #end for +#end if + +#if $rep_param_rm_res: +-rm_res + #for token in $rep_param_rm_res: + #if " " in str(token): + "$token.param_rm_res" + #else + $token.param_rm_res + #end if + #end for +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively. + +The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'. +Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'. + +Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PDBDownload.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PDBDownload.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,49 @@ + + + + + retrieve pdb-file from pdb.org + + PDBDownload + macros.xml + + + + PDBDownload + +#if $param_id: + -id "$param_id" +#end if +#if $param_o: + -o $param_o +#end if +#if $param_p: + -p "$param_p" +#end if + + + + + + + + + + + + + + + + + + + + + + + + Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PDBRMSDCalculator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PDBRMSDCalculator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,78 @@ + + + + + computes RMSD between protein poses + + PDBRMSDCalculator + macros.xml + + + + PDBRMSDCalculator + +#if $param_i_pdb: + -i_pdb $param_i_pdb +#end if +#if $param_i_query: + -i_query $param_i_query +#end if +#if $param_i_type: + -i_type + #if " " in str($param_i_type): + "$param_i_type" + #else + $param_i_type + #end if +#end if +#if $param_o: + -o $param_o +#end if +#if $param_scope: + -scope + #if " " in str($param_scope): + "$param_scope" + #else + $param_scope + #end if +#end if +#if $param_rmsd_type: + -rmsd_type + #if " " in str($param_rmsd_type): + "$param_rmsd_type" + #else + $param_rmsd_type + #end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + This tool computes the RMSD between proteins. + +Parameters are either a second input file (i_query) who's type has to be specified (i_type) and can be either a single pdb, a dcd or a transformation file. Optional parameters are the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope). + +Output of this tool is a either the rmsd (in the pdb-pdb case) or a file (-o) containing the RMSD between the first pose and all other poses. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PartialChargesCopy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PartialChargesCopy.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,36 @@ + + + + + transfer part. charges between files + + PartialChargesCopy + macros.xml + + + + PartialChargesCopy + +#if $param_i: + -i $param_i +#end if +#if $param_chr: + -chr $param_chr +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + + This tool copies partial charges from a given file to the conformations read from a different file. +This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PeptideBuilder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PeptideBuilder.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,47 @@ + + + + + build a peptide + + PeptideBuilder + macros.xml + + + + PeptideBuilder + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + This tool creates a peptide by a given torsion file. The amino acids shall be given in three letter code, the phi, psi, and omega angles shall be given in degree. + +Example: + +# aa phi psi omega + +A -180 140 + +C -180 180 + +G -90 -140 + +P -65 -40 0 # cis + +T -120 -90 + +P -78 146 180 # trans + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PocketDetector.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PocketDetector.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,52 @@ + + + + + detect binding pocket + + PocketDetector + macros.xml + + + + PocketDetector + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_o: + -o $param_o +#end if +#if $param_option: + -option $param_option +#end if +#if $param_mol_out: + -mol_out $param_mol_out +#end if + + + + + + + + + + + + This tool tries to detect the binding pocket in which the reference ligand is located. +Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket. + +As input we need: + * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder. + * 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). + +Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PoseIndices2PDB.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PoseIndices2PDB.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,68 @@ + + + + + converts pose indices into PDB files + + PoseIndices2PDB + macros.xml + + + + PoseIndices2PDB + +#if $param_i_clust: + -i_clust $param_i_clust +#end if +#if $param_i_trans: + -i_trans $param_i_trans +#end if +#if $param_i_pdb: + -i_pdb $param_i_pdb +#end if +#if $param_o: + -o $param_o +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_id: + -o_id "$adv_opts.param_o_id" +#end if + #if $adv_opts.param_o_dir: + -o_dir "$adv_opts.param_o_dir" +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool converts all pose indices from a given transformation file and the corresponding reference PDBFile into separate PDBFiles. + +Parameters are the input pose index file (-i_clust), the original transformation file (-i_trans), the corresponding reference pdb file (-i_pdb) and a naming schema for the resulting pdb files (-o). + +Output of this tool is a set of PDBFiles representing the docking poses belonging to the given input cluster. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/Predictor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/Predictor.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,40 @@ + + + + + predict activities with QSAR model + + Predictor + macros.xml + + + + Predictor + +#if $param_i: + -i $param_i +#end if +#if $param_dat: + -dat $param_dat +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + + This tool predictes the response values of compounds in the given data-file using the specified QSAR model. + +Input of this tool is a model-file as generated by ModelCreator or FeatureSelector and a data-file generated by InputReader. + +Output of this tool (as specified by '-o') is a text file containing the predicted and, if any, the expected response values in one column each. +If you would prefer to use molecule files (sdf,mol2,drf) for input and output, please use the tool MolPredictor instead of this one. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PropertyModifier.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PropertyModifier.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,83 @@ + + + + + modify molecule property tags + + PropertyModifier + macros.xml + + + + PropertyModifier + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_mode: + -mode + #if " " in str($param_mode): + "$param_mode" + #else + $param_mode + #end if +#end if +#if $param_name: + -name "$param_name" +#end if +#if $param_value: + -value "$param_value" +#end if +#if $param_new_name: + -new_name "$param_new_name" +#end if +#if $param_rm: + -rm $param_rm +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + With this tools you can add, rename or delete molecule property tags. +These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule. +The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/PropertyPlotter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/PropertyPlotter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,62 @@ + + + + + plot molecule properties + + PropertyPlotter + macros.xml + + + + PropertyPlotter + +#if $param_i: + -i $param_i +#end if +#if $param_p1: + -p1 "$param_p1" +#end if +#if $param_p2: + -p2 "$param_p2" +#end if +#if $param_o: + -o $param_o +#end if +#if $param_quiet: + -quiet $param_quiet +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + PropertyPlotter can be used to generate distribution- or scatter-plots of data contained in molecule property-tags. + +In case you want to create a scatter-plot, specify the name of both property-tags to be used with '-p1' and '-p2'. If you want to generate a distribution plot, just specify '-p1'. +The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. + +The output of this tool is a plot in form of an eps or png-file (as chosen). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ProteinCheck.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ProteinCheck.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,44 @@ + + + + + quality check for proteins structures + + ProteinCheck + macros.xml + + + + ProteinCheck + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_bc: + -bc $param_bc +#end if + + + + + + + + + + Check a given protein structure for the following errors: + * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem) + * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked. + * each atom must have a valid assigned element + * the protein must be protonated (since this is necessary for docking/(re-)scoring). + * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring) + * there may be no senseless temperature factors (<1 or >100) + * there may be no sterical clashes between atoms + +A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ProteinProtonator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ProteinProtonator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,39 @@ + + + + + protonate protein structures + + ProteinProtonator + macros.xml + + + + ProteinProtonator + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_ph: + -ph $param_ph +#end if + + + + + + + + + + ProteinProtonator allows you add hydrogens to a protein structure. + +Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed. + +Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/RMSDCalculator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/RMSDCalculator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,44 @@ + + + + + calculate RMSD between ligand poses + + RMSDCalculator + macros.xml + + + + RMSDCalculator + +#if $param_i: + -i $param_i +#end if +#if $param_org: + -org $param_org +#end if +#if $param_o: + -o $param_o +#end if +#if $param_quiet: + -quiet $param_quiet +#end if + + + + + + + + + + + This tool calculates the RMSD between different conformations of the same molecule. + +This tool can be used to evaluate the differences between ligand poses taken from co-crystal structures, e.g. generated by a docking run. +Note:Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other. + +Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/RemoveWater.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/RemoveWater.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,31 @@ + + + + + removes water from PDB file + + RemoveWater + macros.xml + + + + RemoveWater + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + This tool removes water from a given pdb file. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ResidueChecker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ResidueChecker.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,80 @@ + + + + + check residues to debug a protein structure wrt to PDB conventions + + ResidueChecker + macros.xml + + + + ResidueChecker + +#if $param_pdb: + -pdb $param_pdb +#end if +#if $param_norm_names: + -norm_names $param_norm_names +#end if +#if $param_build_bonds: + -build_bonds $param_build_bonds +#end if +#if $param_frag_reconstruct: + -frag_reconstruct $param_frag_reconstruct +#end if +#if $param_extra_atoms: + -extra_atoms $param_extra_atoms +#end if +#if $param_bond_length: + -bond_length $param_bond_length +#end if +#if $param_int_net_charge: + -int_net_charge $param_int_net_charge +#end if +#if $param_large_charges: + -large_charges $param_large_charges +#end if +#if $param_large_net_charge: + -large_net_charge $param_large_net_charge +#end if +#if $param_overlapping_atoms: + -overlapping_atoms $param_overlapping_atoms +#end if +#if $param_nan_positions: + -nan_positions $param_nan_positions +#end if +#if $param_elements: + -elements $param_elements +#end if +#if $param_dublicate_atom_names: + -dublicate_atom_names $param_dublicate_atom_names +#end if +#if $param_unknown_residues: + -unknown_residues $param_unknown_residues +#end if + + + + + + + + + + + + + + + + + + + + + + This tool checks the residues of a pdb file wrt. common inconsistencies such as missing atoms or suspicious distances. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/SLICK.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/SLICK.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,84 @@ + + + + + scoring protein-carbohydrate interactions + + SLICK + macros.xml + + + + SLICK + +#if $param_rec: + -rec $param_rec +#end if +#if $param_lig: + -lig $param_lig +#end if +#if $param_cr: + -cr $param_cr +#end if +#if $param_pr: + -pr $param_pr +#end if +#if $param_lj: + -lj $param_lj +#end if +#if $param_op: + -op $param_op +#end if +#if $param_v: + -v $param_v +#end if +#if $param_s: + -s $param_s +#end if +#if $param_t: + -t $param_t +#end if +#if $param_E: + -E $param_E +#end if +#if $param_S: + -S $param_S +#end if +#if $param_u: + -u $param_u +#end if +#if $param_n: + -n $param_n +#end if +#if $param_N: + -N $param_N +#end if +#if $param_log: + -log $param_log +#end if + + + + + + + + + + + + + + + + + + + + + + + This tool calculates the SLICKEnergy / SLICK Score for protein-carbohydrate complexes. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/ScoreAnalyzer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/ScoreAnalyzer.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,98 @@ + + + + + generate ROC or enrichment plots + + ScoreAnalyzer + macros.xml + + + + ScoreAnalyzer + +#if $param_mode: + -mode + #if " " in str($param_mode): + "$param_mode" + #else + $param_mode + #end if +#end if +#if $param_title: + -title "$param_title" +#end if +#if $param_o: + -o $param_o +#end if +#if $param_i: + -i $param_i +#end if +#if $param_s: + -s "$param_s" +#end if +#if $param_e: + -e "$param_e" +#end if +#if $param_t: + -t "$param_t" +#end if +#if $param_b: + -b $param_b +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring. + +The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'. +The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. + +The output of this tool is a plot in form of an eps or png-file (as chosen). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/SeparateMolecules.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/SeparateMolecules.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,44 @@ + + + + + Split each multi molecule entry to separate single molecule entries + + SeperateMolecules + macros.xml + + + + SeperateMolecules + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_min_atoms: + -min_atoms $param_min_atoms +#end if +#if $param_all: + -all $param_all +#end if + + + + + + + + + + + This tool splits each molecule entry contained in a structure file (mol, sdf, mol2) into possibly multiple molecule entries, so that the new entries contain only a single connected molecule. The results will always be written to a single structure file in the same format as the input format, or a sdf-file in the case of a mol input file. The tool works with the given bond information, which needs to be correct. + +Standard behaviour: only the largest molecule from each entry is retained ('largest' according to the number of atoms). + +Optional parameters: +Retain all molecules contained in a molecule entry ('-all'). Alternatively the minimal number of atoms required for a molecule to be kept can be specified ('-min_atoms'). + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/SideChainGridBuilder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/SideChainGridBuilder.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,39 @@ + + + + + build side chain grid + + SideChainGridBuilder + macros.xml + + + + SideChainGridBuilder + +#if $param_param: + -param $param_param +#end if +#if $param_d: + -d "$param_d" +#end if + + + + + + + + + + + + + + + + + This tool precalculates a side chain grid. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/SimilarityAnalyzer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/SimilarityAnalyzer.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,55 @@ + + + + + analyze similarity between molecule files + + SimilarityAnalyzer + macros.xml + + + + SimilarityAnalyzer + +#if $param_i1: + -i1 $param_i1 +#end if +#if $param_i2: + -i2 $param_i2 +#end if +#if $param_o: + -o $param_o +#end if +#if $param_title: + -title "$param_title" +#end if +#if $param_quiet: + -quiet $param_quiet +#end if + + + + + + + + + + + + + + + + + + + This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result. + +Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure. +The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. + +The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/SimpleRescorer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/SimpleRescorer.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,119 @@ + + + + + rescore docking results + + SimpleRescorer + macros.xml + + + + SimpleRescorer + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_option: + -option $param_option +#end if +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_function: + -function + #if " " in str($param_function): + "$param_function" + #else + $param_function + #end if +#end if +#if $param_rm: + -rm $param_rm +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool rescores docking output poses. +A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified). + +As input we need: + * a file containing a protonated protein in pdb-format + * 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 the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein. + +Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/SpatialConstraintDefiner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/SpatialConstraintDefiner.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,60 @@ + + + + + define spatial constraint + + SpatialConstraintDefiner + macros.xml + + + + SpatialConstraintDefiner + +#if $param_option: + -option $param_option +#end if +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if +#if $param_n: + -n $param_n +#end if +#if $param_p: + -p $param_p +#end if + + + + + + + + + + + + + + + + This tool allows to define spatial constraints for docking or scoring. + +For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint. +Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this. + +Output of this tool is a ini-file that contains the desired spatial constraint. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/TaGRes-train.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/TaGRes-train.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,139 @@ + + + + + Target-specific Grid-Rescoring, training + + TaGResTrain + macros.xml + + + + TaGResTrain + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_option: + -option $param_option +#end if +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_method: + -method + #if " " in str($param_method): + "$param_method" + #else + $param_method + #end if +#end if +#if $param_function: + -function + #if " " in str($param_function): + "$param_function" + #else + $param_function + #end if +#end if +#if $param_exp: + -exp "$param_exp" +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool generates a model for Target-specific Grid-Rescoring (TaGRes). +As input we need: + + * a file containing a protonated protein in pdb-format + * 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 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 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. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/TaGRes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/TaGRes.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,142 @@ + + + + + Target-specific Grid-Rescoring + + TaGRes + macros.xml + + + + TaGRes + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_option: + -option $param_option +#end if +#if $param_i: + -i $param_i +#end if +#if $param_mod: + -mod $param_mod +#end if +#if $param_tf: + -tf $param_tf +#end if +#if $param_o: + -o $param_o +#end if +#if $param_method: + -method + #if " " in str($param_method): + "$param_method" + #else + $param_method + #end if +#end if +#if $param_function: + -function + #if " " in str($param_function): + "$param_function" + #else + $param_function + #end if +#end if +#if $param_rm: + -rm $param_rm +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool rescores docking output poses using Target-specific Grid-Rescoring. +Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool. +As input TaGRes needs: + + * a file containing a protonated protein in pdb-format + * 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 the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein. + * a regression model file as generated by TaGRes-train for same protein target than the one specified here. + +TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy. + +Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/Trajectory2RigidTransformation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/Trajectory2RigidTransformation.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,39 @@ + + + + + converts a trajectory file into a rigid transformation file + + Trajectory2RigidTransformation + macros.xml + + + + Trajectory2RigidTransformation + +#if $param_i_dcd: + -i_dcd $param_i_dcd +#end if +#if $param_i_pdb: + -i_pdb $param_i_pdb +#end if +#if $param_o: + -o $param_o +#end if + + + + + + + + + + This tool converts SnapShots of a given TrajectoryFile and the reference PDBFile into a rigid transformation file. + +Parameters are the input SnapShots as TrajectoryFile (-i_dcd), the corresponding reference pdb file that was originally used to create the TrajectoryFile (-i_pdb) and a naming schema for the resulting transformation file (-o). + +Output of this tool is a file storing each given SnapShot as rigid transformation per line. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/TrajectoryFile2PDBSplitter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/TrajectoryFile2PDBSplitter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,64 @@ + + + + + splits SnapShots into PDB files + + TrajectoryFile2PDBSplitter + macros.xml + + + + TrajectoryFile2PDBSplitter + +#if $param_i_traj: + -i_traj $param_i_traj +#end if +#if $param_i_pdb: + -i_pdb $param_i_pdb +#end if +#if $param_o: + -o $param_o +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_id: + -o_id "$adv_opts.param_o_id" +#end if + #if $adv_opts.param_o_dir: + -o_dir "$adv_opts.param_o_dir" +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool splits SnapShots of a given TrajectoryFile and the reference PDBFile into separate PDBFiles. + +Parameters are the input SnapShots as TrajectoryFile (-i_traj), the corresponding reference pdb file that was originally used to create the TrajectoryFile (-i_pdb) and a naming schema for the results (-o). + +Output of this tool is a number of PDBFiles each containing one SnapShot. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/Validator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/Validator.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,51 @@ + + + + + evaluate quality of a QSAR model + + Validator + macros.xml + + + + Validator + +#if $param_i: + -i $param_i +#end if +#if $param_dat: + -dat $param_dat +#end if +#if $param_o: + -o $param_o +#end if +#if $param_type: + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if +#end if + + + + + + + + + + + + + + + + Validator evaluates the quality of a QSAR model. + +The validation technique to be used for this can selected by '-type'. As input this tools need a model-file as generate by InputReader or FeatureSelector and a data-file generated by InputReader containing the prediction data set. Note that the latter must contain response values so that predictions done by the supplied model can be compared to those values by the validation method. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/WaterFinder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/WaterFinder.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,116 @@ + + + + + find strongly bound waters + + WaterFinder + macros.xml + + + + WaterFinder + +#if $param_rec: + -rec $param_rec +#end if +#if $param_rl: + -rl $param_rl +#end if +#if $param_option: + -option $param_option +#end if +#if $param_wat: + -wat $param_wat +#end if +#if $param_o: + -o $param_o +#end if +#if $param_ai: + -ai $param_ai +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ScoringFunction_filename: + -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cuton: + -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton +#end if + #if $adv_opts.param_ScoringFunction_electrostatic_cutoff: + -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff +#end if + #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap: + -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_ignore_H_clashes: + -ScoringFunction:ignore_H_clashes +#end if + #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap: + -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap +#end if + #if $adv_opts.param_ScoringFunction_burial_depth_scale: + -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale +#end if + #if $adv_opts.param_ScoringFunction_vdw_cutoff: + -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff +#end if + #if $adv_opts.param_ScoringFunction_nonbonded_cutoff: + -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_size: + -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size +#end if + #if $adv_opts.param_ScoringFunction_vdw_cuton: + -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton +#end if + #if $adv_opts.param_ScoringFunction_hashgrid_resolution: + -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + This tool searches for crystal waters that + * either interact very strongly with the receptor + * or that interact strongly with receptor and reference ligand, + thus functioning as a water bridge. + +Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done. + +As input we need: + * a file containing a protonated protein in pdb-format. + This file should contain water molecules that are to be evaluated by this tool. + However, you can also use a separate pdb-file as input for the water molecules (see below). + * 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). + * optionally a file in pdb-format containing water molecules. + If you specify such a file , all water molecules appearing in the + protein input-file (if any) will be ignored. + +Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules. + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/datatypes_conf.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/macros.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,31 @@ + + + + + + @EXECUTABLE@ + + + + + + + + + + + + + + + + + + + + + + + diff -r 31013b5cd066 -r 605370bc1def galaxy_stubs/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/tool_conf.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,89 @@ + + +

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