Mercurial > repos > luis > ball
changeset 2:605370bc1def draft default tip
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--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="AddMissingAtoms" name="AddMissingAtoms" version="1.1.0"> + <description>add missing atoms to protein structures</description> + <macros> + <token name="@EXECUTABLE@">AddMissingAtoms</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_opt_hyd" type="integer" min="0" max="1" optional="True" value="0" label="optimize the positions of hydrogens" help="(-opt_hyd) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Rescoring]--> +<tool id="AntitargetRescorer" name="AntitargetRescorer" version="1.1.0"> + <description>rescore w/ anti-target dock-results</description> + <macros> + <token name="@EXECUTABLE@">AntitargetRescorer</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_t" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file w/ target dock-results" help="(-t) "/> + <param name="param_at" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file w/ anti-target dock-results" help="(-at) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_t" format="input"/> + </outputs> + <help>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'. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="AutoModel" name="AutoModel" version="1.1.0"> + <description>automatically find best QSAR model</description> + <macros> + <token name="@EXECUTABLE@">AutoModel</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input data-file" help="(-i) "/> + <param name="param_min_quality" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="minimal desired quality (default: 0.3)" help="(-min_quality) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="mod"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="BindingDBCleaner" name="BindingDBCleaner" version="1.1.0"> + <description>fix bindingdb.org downloads</description> + <macros> + <token name="@EXECUTABLE@">BindingDBCleaner</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_type" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="type of contained activity values: 'Ki' or 'IC50'" help="(-type) "> + <option value="IC50">IC50</option> + <option value=" Ki"> Ki</option> + </param> + <param name="param_target" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="binding-DB target name" help="(-target) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="BondOrderAssigner" name="BondOrderAssigner" version="1.1.0"> + <description>computes bond order assignments for a ligand </description> + <macros> + <token name="@EXECUTABLE@">BondOrderAssigner</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mol2-file" help="(-i) "/> + <param name="param_max_sol" type="integer" min="0" max="100" optional="True" value="25" label="maximal number of assignments solutions to compute" help="(-max_sol) "/> + <param name="param_scr_pen" type="select" optional="True" value="Antechamber" label="penalty table (Antechamber, BALL)" help="(-scr_pen) "> + <option value="Antechamber">Antechamber</option> + <option value=" BALL"> BALL</option> + </param> + <param name="param_non_opt" type="integer" min="0" max="1" optional="True" value="0" label="compute sub-optimal assignments as well" help="(-non_opt) "/> + <expand macro="advanced_options"> + <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>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 + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [ForceFields]--> +<tool id="CalculateBindingFreeEnergy" name="CalculateBindingFreeEnergy" version="1.1.0"> + <description>calculate binding energy of two proteins using AMBER</description> + <macros> + <token name="@EXECUTABLE@">CalculateBindingFreeEnergy</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>CalculateBindingFreeEnergy + +#if $param_pdb_a: + -pdb_a $param_pdb_a +#end if +#if $param_pdb_b: + -pdb_b $param_pdb_b +#end if +</command> + <inputs> + <param name="param_pdb_a" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="first input pdb file" help="(-pdb_a) "/> + <param name="param_pdb_b" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="second input pdb file" help="(-pdb_b) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>This tool computes the binding energy of two given pdb files using the AMBER force field. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [ForceFields]--> +<tool id="CalculateEnergy" name="CalculateEnergy" version="1.1.0"> + <description>calculate free energy of a protein </description> + <macros> + <token name="@EXECUTABLE@">CalculateEnergy</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> + <param name="param_force_field" type="select" optional="True" value="AMBER" label="force field (AMBER, MMFF94)" help="(-force_field) "> + <option value="AMBER">AMBER</option> + <option value=" MMFF94"> MMFF94</option> + </param> + <param name="param_non_bond_cutoff" type="float" value="20.0" label="cutoff radius in calculations of nonbonded interactions" help="(-non_bond_cutoff) "/> + <param name="param_elec_stat_cuton" type="float" value="13.0" label="electrostatic cuton" help="(-elec_stat_cuton) "/> + <param name="param_elec_stat_cutoff" type="float" value="15.0" label="electrostatic cutoff" help="(-elec_stat_cutoff) "/> + <param name="param_dist_dep_dielec" type="integer" min="0" max="1" optional="True" value="0" label="apply distance dependent dielectric constant" help="(-dist_dep_dielec) "/> + <param name="param_overwrite_types" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-empty type names" help="(-overwrite_types) "/> + <param name="param_overwrite_charges" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-zero charges" help="(-overwrite_charges) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>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 ... ). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [ForceFields]--> +<tool id="CalculateSolvationFreeEnergy" name="CalculateSolvationFreeEnergy" version="1.1.0"> + <description>calculate solvation free energy of a protein using AMBER </description> + <macros> + <token name="@EXECUTABLE@">CalculateSolvationFreeEnergy</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> + <param name="param_epsilon_medium" type="float" value="0.0" label="dielectric constant in medium" help="(-epsilon_medium) "/> + <param name="param_epsilon_vacuum" type="float" value="1.0" label="dielectric constant in vacuum" help="(-epsilon_vacuum) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Get Data]--> +<tool id="CombiLibGenerator" name="CombiLibGenerator" version="1.1.0"> + <description>generate combinatorial lib</description> + <macros> + <token name="@EXECUTABLE@">CombiLibGenerator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>CombiLibGenerator + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +</command> + <inputs> + <param name="param_i" type="data" format="txt" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input combi-lib file" help="(-i) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="ConstraintsFinder" name="ConstraintsFinder" version="1.1.0"> + <description>find strongly interacting residues</description> + <macros> + <token name="@EXECUTABLE@">ConstraintsFinder</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="ini"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="Converter" name="Converter" version="1.1.0"> + <description>interconvert molecular file-formats</description> + <macros> + <token name="@EXECUTABLE@">Converter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input filename" help="(-i) "/> + <param name="param_if" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input format" help="(-if) "> + <option value="mol2">mol2</option> + <option value=" sdf"> sdf</option> + <option value=" drf"> drf</option> + <option value=" pdb"> pdb</option> + <option value=" ac"> ac</option> + <option value=" ent"> ent</option> + <option value=" brk"> brk</option> + <option value=" hin"> hin</option> + <option value=" mol"> mol</option> + <option value=" xyz"> xyz</option> + <option value=" mol2.gz"> mol2.gz</option> + <option value=" sdf.gz"> sdf.gz</option> + <option value=" drf.gz"> drf.gz</option> + <option value=" pdb.gz"> pdb.gz</option> + <option value=" ac.gz"> ac.gz</option> + <option value=" ent.gz"> ent.gz</option> + <option value=" brk.gz"> brk.gz</option> + <option value=" hin.gz"> hin.gz</option> + <option value=" mol.gz"> mol.gz</option> + <option value=" xyz.gz"> xyz.gz</option> + </param> + <param name="param_of" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="output format" help="(-of) "> + <option value="mol2">mol2</option> + <option value=" sdf"> sdf</option> + <option value=" drf"> drf</option> + <option value=" pdb"> pdb</option> + <option value=" ac"> ac</option> + <option value=" ent"> ent</option> + <option value=" brk"> brk</option> + <option value=" hin"> hin</option> + <option value=" mol"> mol</option> + <option value=" xyz"> xyz</option> + <option value=" mol2.gz"> mol2.gz</option> + <option value=" sdf.gz"> sdf.gz</option> + <option value=" drf.gz"> drf.gz</option> + <option value=" pdb.gz"> pdb.gz</option> + <option value=" ac.gz"> ac.gz</option> + <option value=" ent.gz"> ent.gz</option> + <option value=" brk.gz"> brk.gz</option> + <option value=" hin.gz"> hin.gz</option> + <option value=" mol.gz"> mol.gz</option> + <option value=" xyz.gz"> xyz.gz</option> + </param> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Structure Creation]--> +<tool id="CrystalGenerator" name="CrystalGenerator" version="VERSION"> + <description>creates crystals</description> + <macros> + <token name="@EXECUTABLE@">CrystalGenerator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-i) "/> + <param name="param_sg" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="space group symbol in Herman-Mauguin notation" help="(-sg) "> + <option value="P 1">P 1</option> + <option value=" P 1-"> P 1-</option> + <option value=" P 2"> P 2</option> + <option value=" P 21"> P 21</option> + <option value=" C 2"> C 2</option> + <option value=" P M"> P M</option> + <option value=" P C"> P C</option> + <option value=" C M"> C M</option> + <option value=" C C"> C C</option> + <option value=" P 2/M"> P 2/M</option> + <option value=" P 21/M"> P 21/M</option> + <option value=" C 2/M"> C 2/M</option> + <option value=" P 2/C"> P 2/C</option> + <option value=" P 21/C"> P 21/C</option> + <option value=" C 2/C"> C 2/C</option> + <option value=" P 2 2 2"> P 2 2 2</option> + <option value=" P 2 2 21"> P 2 2 21</option> + <option value=" P 21 21 2"> P 21 21 2</option> + <option value=" P 21 21 21"> P 21 21 21</option> + <option value=" C 2 2 21"> C 2 2 21</option> + <option value=" C 2 2 2"> C 2 2 2</option> + <option value=" F 2 2 2"> F 2 2 2</option> + <option value=" I 2 2 2"> I 2 2 2</option> + <option value=" I 21 21 21"> I 21 21 21</option> + <option value=" P M M 2"> P M M 2</option> + <option value=" P M C 21"> P M C 21</option> + <option value=" P C C 2"> P C C 2</option> + <option value=" P M A 2"> P M A 2</option> + <option value=" P C A 21"> P C A 21</option> + <option value=" P N C 2"> P N C 2</option> + <option value=" P M N 21"> P M N 21</option> + <option value=" P B A 2"> P B A 2</option> + <option value=" P N A 21"> P N A 21</option> + <option value=" P N N 2"> P N N 2</option> + <option value=" C M M 2"> C M M 2</option> + <option value=" C M C 21"> C M C 21</option> + <option value=" C C C 2"> C C C 2</option> + <option value=" A M M 2"> A M M 2</option> + <option value=" A B M 2"> A B M 2</option> + <option value=" A M A 2"> A M A 2</option> + <option value=" A B A 2"> A B A 2</option> + <option value=" F M M 2"> F M M 2</option> + <option value=" F D D 2"> F D D 2</option> + <option value=" I M M 2"> I M M 2</option> + <option value=" I B A 2"> I B A 2</option> + <option value=" I M A 2"> I M A 2</option> + <option value=" P M M M"> P M M M</option> + <option value=" P N N N"> P N N N</option> + <option value=" P C C M"> P C C M</option> + <option value=" P B A N"> P B A N</option> + <option value=" P M M A"> P M M A</option> + <option value=" P N N A"> P N N A</option> + <option value=" P M N A"> P M N A</option> + <option value=" P C C A"> P C C A</option> + <option value=" P B A M"> P B A M</option> + <option value=" P C C N"> P C C N</option> + <option value=" P B C M"> P B C M</option> + <option value=" P N N M"> P N N M</option> + <option value=" P M M N"> P M M N</option> + <option value=" P B C N"> P B C N</option> + <option value=" P B C A"> P B C A</option> + <option value=" P N M A"> P N M A</option> + <option value=" C M C M"> C M C M</option> + <option value=" C M C A"> C M C A</option> + <option value=" C M M M"> C M M M</option> + <option value=" C C C M"> C C C M</option> + <option value=" C M M A"> C M M A</option> + <option value=" C C C A"> C C C A</option> + <option value=" F M M M"> F M M M</option> + <option value=" F D D D"> F D D D</option> + <option value=" I M M M"> I M M M</option> + <option value=" I B A M"> I B A M</option> + <option value=" I B C A"> I B C A</option> + <option value=" I M M A"> I M M A</option> + <option value=" P 4"> P 4</option> + <option value=" P 41"> P 41</option> + <option value=" P 42"> P 42</option> + <option value=" P 43"> P 43</option> + <option value=" I 4"> I 4</option> + <option value=" I 41"> I 41</option> + <option value=" P -4"> P -4</option> + <option value=" I -4"> I -4</option> + <option value=" P 4/M"> P 4/M</option> + <option value=" P 42/M"> P 42/M</option> + <option value=" P 4/N"> P 4/N</option> + <option value=" P 42/N"> P 42/N</option> + <option value=" I 4/M"> I 4/M</option> + <option value=" I 41/A"> I 41/A</option> + <option value=" P 4 2 2"> P 4 2 2</option> + <option value=" P 4 21 2"> P 4 21 2</option> + <option value=" P 41 2 2"> P 41 2 2</option> + <option value=" P 41 21 2"> P 41 21 2</option> + <option value=" P 42 2 2"> P 42 2 2</option> + <option value=" P 42 21 2"> P 42 21 2</option> + <option value=" P 43 2 2"> P 43 2 2</option> + <option value=" P 43 21 2"> P 43 21 2</option> + <option value=" I 4 2 2"> I 4 2 2</option> + <option value=" I 41 2 2"> I 41 2 2</option> + <option value=" P 4 M M"> P 4 M M</option> + <option value=" P 4 B M"> P 4 B M</option> + <option value=" P 42 C M"> P 42 C M</option> + <option value=" P 42 N M"> P 42 N M</option> + <option value=" P 4 C C"> P 4 C C</option> + <option value=" P 4 N C"> P 4 N C</option> + <option value=" P 42 M C"> P 42 M C</option> + <option value=" P 42 B C"> P 42 B C</option> + <option value=" I 4 M M"> I 4 M M</option> + <option value=" I 4 C M"> I 4 C M</option> + <option value=" I 41 M D"> I 41 M D</option> + <option value=" I 41 C D"> I 41 C D</option> + <option value=" P -4 2 M"> P -4 2 M</option> + <option value=" P -4 2 C"> P -4 2 C</option> + <option value=" P -4 21 M"> P -4 21 M</option> + <option value=" P -4 21 C"> P -4 21 C</option> + <option value=" P -4 M 2"> P -4 M 2</option> + <option value=" P -4 C 2"> P -4 C 2</option> + <option value=" P -4 B 2"> P -4 B 2</option> + <option value=" P -4 N 2"> P -4 N 2</option> + <option value=" I -4 M 2"> I -4 M 2</option> + <option value=" I -4 C 2"> I -4 C 2</option> + <option value=" I -4 2 M"> I -4 2 M</option> + <option value=" I -4 2 D"> I -4 2 D</option> + <option value=" P 4/M M M"> P 4/M M M</option> + <option value=" P 4/M C C"> P 4/M C C</option> + <option value=" P 4/N B M"> P 4/N B M</option> + <option value=" P 4/N N C"> P 4/N N C</option> + <option value=" P 4/M B M"> P 4/M B M</option> + <option value=" P 4/M N C"> P 4/M N C</option> + <option value=" P 4/N M M"> P 4/N M M</option> + <option value=" P 4/N C C"> P 4/N C C</option> + <option value=" P 42/M M C"> P 42/M M C</option> + <option value=" P 42/M C M"> P 42/M C M</option> + <option value=" P 42/N B C"> P 42/N B C</option> + <option value=" P 42/N N M"> P 42/N N M</option> + <option value=" P 42/M B C"> P 42/M B C</option> + <option value=" P 42/M N M"> P 42/M N M</option> + <option value=" P 42/N M C"> P 42/N M C</option> + <option value=" P 42/N C M"> P 42/N C M</option> + <option value=" I 4/M M M"> I 4/M M M</option> + <option value=" I 4/M C M"> I 4/M C M</option> + <option value=" I 41/A M D"> I 41/A M D</option> + <option value=" I 41/A C D"> I 41/A C D</option> + <option value=" P 3"> P 3</option> + <option value=" P 31"> P 31</option> + <option value=" P 32"> P 32</option> + <option value=" R 3"> R 3</option> + <option value=" P -3"> P -3</option> + <option value=" R -3"> R -3</option> + <option value=" P 3 1 2"> P 3 1 2</option> + <option value=" P 3 2 1"> P 3 2 1</option> + <option value=" P 31 1 2"> P 31 1 2</option> + <option value=" P 31 2 1"> P 31 2 1</option> + <option value=" P 32 1 2"> P 32 1 2</option> + <option value=" P 32 2 1"> P 32 2 1</option> + <option value=" R 3 2"> R 3 2</option> + <option value=" P 3 M 1"> P 3 M 1</option> + <option value=" P 3 1 M"> P 3 1 M</option> + <option value=" P 3 C 1"> P 3 C 1</option> + <option value=" P 3 1 C"> P 3 1 C</option> + <option value=" R 3 M"> R 3 M</option> + <option value=" R 3 C"> R 3 C</option> + <option value=" P -3 1 M"> P -3 1 M</option> + <option value=" P -3 1 C"> P -3 1 C</option> + <option value=" P -3 M 1"> P -3 M 1</option> + <option value=" P -3 C 1"> P -3 C 1</option> + <option value=" R -3 M"> R -3 M</option> + <option value=" R -3 C"> R -3 C</option> + <option value=" P 6"> P 6</option> + <option value=" P 61"> P 61</option> + <option value=" P 65"> P 65</option> + <option value=" P 62"> P 62</option> + <option value=" P 64"> P 64</option> + <option value=" P 63"> P 63</option> + <option value=" P -6"> P -6</option> + <option value=" P 6/M"> P 6/M</option> + <option value=" P 63/M"> P 63/M</option> + <option value=" P 6 2 2"> P 6 2 2</option> + <option value=" P 61 2 2"> P 61 2 2</option> + <option value=" P 65 2 2"> P 65 2 2</option> + <option value=" P 62 2 2"> P 62 2 2</option> + <option value=" P 64 2 2"> P 64 2 2</option> + <option value=" P 63 2 2"> P 63 2 2</option> + <option value=" P 6 M M"> P 6 M M</option> + <option value=" P 6 C C"> P 6 C C</option> + <option value=" P 63 C M"> P 63 C M</option> + <option value=" P 63 M C"> P 63 M C</option> + <option value=" P -6 M 2"> P -6 M 2</option> + <option value=" P -6 C 2"> P -6 C 2</option> + <option value=" P -6 2 M"> P -6 2 M</option> + <option value=" P -6 2 C"> P -6 2 C</option> + <option value=" P 6/M M M"> P 6/M M M</option> + <option value=" P 6/M C C"> P 6/M C C</option> + <option value=" P 63/M C M"> P 63/M C M</option> + <option value=" P 63/M M C"> P 63/M M C</option> + <option value=" P 2 3"> P 2 3</option> + <option value=" F 2 3"> F 2 3</option> + <option value=" I 2 3"> I 2 3</option> + <option value=" P 21 3"> P 21 3</option> + <option value=" I 21 3"> I 21 3</option> + <option value=" P M -3"> P M -3</option> + <option value=" P N -3"> P N -3</option> + <option value=" F M -3"> F M -3</option> + <option value=" F D -3"> F D -3</option> + <option value=" I M -3"> I M -3</option> + <option value=" P A -3"> P A -3</option> + <option value=" I A -3"> I A -3</option> + <option value=" P 4 3 2"> P 4 3 2</option> + <option value=" P 42 3 2"> P 42 3 2</option> + <option value=" F 4 3 2"> F 4 3 2</option> + <option value=" F 41 3 2"> F 41 3 2</option> + <option value=" I 4 3 2"> I 4 3 2</option> + <option value=" P 43 3 2"> P 43 3 2</option> + <option value=" P 41 3 2"> P 41 3 2</option> + <option value=" I 41 3 2"> I 41 3 2</option> + <option value=" P -4 3 M"> P -4 3 M</option> + <option value=" F 4 -3 M"> F 4 -3 M</option> + <option value=" I -4 3 M"> I -4 3 M</option> + <option value=" P -4 3 N"> P -4 3 N</option> + <option value=" F -4 3 C"> F -4 3 C</option> + <option value=" I -4 3 D"> I -4 3 D</option> + <option value=" P M -3 M"> P M -3 M</option> + <option value=" P N -3 N"> P N -3 N</option> + <option value=" P M -3 N"> P M -3 N</option> + <option value=" P N -3 M"> P N -3 M</option> + <option value=" F M -3 M"> F M -3 M</option> + <option value=" F M -3 C"> F M -3 C</option> + <option value=" F D -3 M"> F D -3 M</option> + <option value=" F D -3 C"> F D -3 C</option> + <option value=" I M -3 M"> I M -3 M</option> + <option value=" I A -3 D"> I A -3 D</option> + <option value=" B 2"> B 2</option> + <option value=" P 1 1 21"> P 1 1 21</option> + <option value=" P 2 21 21"> P 2 21 21</option> + <option value=" P 21 2 21"> P 21 2 21</option> + <option value=" I 1 2 1"> I 1 2 1</option> + </param> + <param name="param_axis_a" type="float" value="0.0" label="cell axis a" help="(-axis_a) "/> + <param name="param_axis_b" type="float" value="0.0" label="cell axis" help="(-axis_b) "/> + <param name="param_axis_c" type="float" value="0.0" label="cell axis c" help="(-axis_c) "/> + <param name="param_angle_alpha" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle alpha" help="(-angle_alpha) "/> + <param name="param_angle_beta" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle beta" help="(-angle_beta) "/> + <param name="param_angle_gamma" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle gamma" help="(-angle_gamma) "/> + <param name="param_from_uc_a" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index a" help="(-from_uc_a) "/> + <param name="param_from_uc_b" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index" help="(-from_uc_b) "/> + <param name="param_from_uc_c" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index c" help="(-from_uc_c) "/> + <param name="param_to_uc_a" type="integer" value="0" label="to unit cell index a" help="(-to_uc_a) "/> + <param name="param_to_uc_b" type="integer" value="0" label="to unit cell index" help="(-to_uc_b) "/> + <param name="param_to_uc_c" type="integer" value="0" label="to unit cell index c" help="(-to_uc_c) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>TODO: Manual + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="DockPoseClustering" name="DockPoseClustering" version="1.1.0"> + <description>clusters docking poses </description> + <macros> + <token name="@EXECUTABLE@">DockPoseClustering</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i_pdb) "/> + <param name="param_i_dcd" type="data" format="dcd" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input dcd-file" help="(-i_dcd) "/> + <param name="param_i_trans" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="or input transformation file for rigid rmsd clustering" help="(-i_trans) "/> + <param name="param_rmsd_cutoff" type="float" min="0.0" max="100.0" optional="True" value="5.0" label="minimal rmsd between the final clusters (default 5.0)" help="(-rmsd_cutoff) "/> + <param name="param_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for clustering (CLINK_DEFAYS, CLINK_ALTHAUS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-alg) "> + <option value="CLINK_DEFAYS">CLINK_DEFAYS</option> + <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option> + <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option> + <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option> + <option value=" SLINK_SIBSON"> SLINK_SIBSON</option> + </param> + <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) "> + <option value="C_ALPHA">C_ALPHA</option> + <option value=" BACKBONE"> BACKBONE</option> + <option value=" ALL_ATOMS"> ALL_ATOMS</option> + </param> + <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) "> + <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option> + <option value=" RIGID_RMSD"> RIGID_RMSD</option> + <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option> + </param> + <param name="param_refine_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for second clustering run (CLINK_DEFAYS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-refine_alg) "> + <option value="CLINK_DEFAYS">CLINK_DEFAYS</option> + <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option> + <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option> + <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option> + <option value=" SLINK_SIBSON"> SLINK_SIBSON</option> + </param> + <param name="param_refine_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for second clustering run (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-refine_rmsd_type) "> + <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option> + <option value=" RIGID_RMSD"> RIGID_RMSD</option> + <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option> + </param> + <param name="param_refine_rmsd_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for rmsd score in second clustering run (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-refine_rmsd_scope) "> + <option value="C_ALPHA">C_ALPHA</option> + <option value=" BACKBONE"> BACKBONE</option> + <option value=" ALL_ATOMS"> ALL_ATOMS</option> + </param> + <param name="param_use_refinement" type="integer" min="0" max="1" optional="True" value="0" label="Apply a second clustering run with different options (-refine_alg <string>, -refine_rmsd_type <string>, and -refine_rmsd_scope <string>)" help="(-use_refinement) "/> + <param name="param_run_serial" type="integer" min="0" max="1" optional="True" value="0" label="force serial excecution, even if parallel execution would be supported by the algorithm" help="(-run_serial) "/> + <expand macro="advanced_options"> + <param name="param_o_dcd_id" type="text" size="30" value="$o_dcd.id" label="output id" help="(-o_dcd_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dcd_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last cluster dcd file (if needed)" help="(-o_dcd_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o_index_list" format="txt"/> + <data name="param_o_score_matrix" format="txt"/> + <data name="param_o_dcd" format="dcd"/> + <data name="param_o_red_dcd" format="dcd"/> + <data name="param_o_cluster_tree" format="dat"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="DockResultMerger" name="DockResultMerger" version="1.1.0"> + <description>merge docking output files</description> + <macros> + <token name="@EXECUTABLE@">DockResultMerger</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input files" help="(-i) "/> + <param name="param_score" type="text" size="30" value="score" label="score property name" help="(-score) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_min" type="float" value="-30.0" label="minimal score value" help="(-min) "/> + <param name="param_max" type="float" value="0.0" label="maximal score value" help="(-max) "/> + <param name="param_k" type="integer" value="20" label="number of output molecules" help="(-k) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files after merging" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="EvenSplit" name="EvenSplit" version="1.1.0"> + <description>generate splits w/ equal property range</description> + <macros> + <token name="@EXECUTABLE@">EvenSplit</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_prop" type="text" size="30" value="binding_free_energy" label="property name" help="(-prop) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_n" type="integer" value="0" label="max. number of compounds to use from input file" help="(-n) "/> + <param name="param_k" type="integer" value="2" label="extract each k'th compound to 2nd output file" help="(-k) "/> + <param name="param_offset" type="integer" value="0" label="offset; extract each (i+offset)%k == 0 to 2nd output file" help="(-offset) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o1" metadata_source="param_i" format="input"/> + <data name="param_o2" metadata_source="param_i" format="input"/> + </outputs> + <help>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'. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="ExtractClustersFromWardTree" name="ExtractClustersFromWardTree" version="1.1.0"> + <description>extracts docking clusters </description> + <macros> + <token name="@EXECUTABLE@">ExtractClustersFromWardTree</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input serialized cluster file" help="(-i) "/> + <param name="param_i_type" type="text" size="30" value="binary" label="input type (binary, text)" help="(-i_type) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_type" type="select" optional="True" value="index_list" label="output type (gv, json, index_list)" help="(-o_type) "> + <option value="gv">gv</option> + <option value=" json"> json</option> + <option value=" index_list"> index_list</option> + </param> + <param name="param_cutoff_type" type="select" optional="True" value="ward_distance" label="cutoff type (ward_distance, num_clusters)" help="(-cutoff_type) "> + <option value="ward_distance">ward_distance</option> + <option value=" num_clusters"> num_clusters</option> + </param> + <param name="param_cut_value" type="float" min="0.0" max="10000.0" optional="True" value="5.0" label="cut value for splitting the given WART tree using the cutoff-type (default 5.0)" help="(-cut_value) "/> + <param name="param_min_size" type="integer" min="1" max="10000" optional="True" value="1" label="minimal size of clusters (default 1)" help="(-min_size) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o_out" format="gv"/> + </outputs> + <help>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 + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="ExtractProteinChains" name="ExtractProteinChains" version="1.1.0"> + <description>separate all chains of a pdb file into separate pdb files</description> + <macros> + <token name="@EXECUTABLE@">ExtractProteinChains</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> + <param name="param_chain_id" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="chain to extract" help="(-chain_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <expand macro="advanced_options"> + <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>This tool splits a pdb file into its chains. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Get Data]--> +<tool id="ExtractProteinSequence" name="ExtractProteinSequence" version="1.1.0"> + <description>extracts fasta sequence</description> + <macros> + <token name="@EXECUTABLE@">ExtractProteinSequence</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file from which to extract" help="(-i) "/> + <param name="param_c" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="chain specifie" help="(-c) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="fasta"/> + </outputs> + <help>This tool extracts the fasta sequence from a given pdb file. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="FeatureSelector" name="FeatureSelector" version="1.1.0"> + <description>run feature-selection on a QSAR model</description> + <macros> + <token name="@EXECUTABLE@">FeatureSelector</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mod" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mod-file" help="(-i) "/> + <param name="param_dat" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="data-file" help="(-dat) "/> + <param name="param_type" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="feature-selection type" help="(-type) "> + <option value="remove_correlated">remove_correlated</option> + <option value=" forward_selection"> forward_selection</option> + <option value=" backward_selection"> backward_selection</option> + <option value=" stepwise_selection"> stepwise_selection</option> + <option value=" twinscan"> twinscan</option> + <option value=" removeLowResponseCorrelation"> removeLowResponseCorrelation</option> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="mod"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Chemoinformatics]--> +<tool id="FingerprintSimilarityClustering" name="FingerprintSimilarityClustering" version="1.1.0"> + <description>fast clustering of compounds using 2D binary fingerprints</description> + <macros> + <token name="@EXECUTABLE@">FingerprintSimilarityClustering</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_t" type="data" format="smi.gz,csv,sdf.gz,sdf,txt.gz,smi,txt,csv.gz" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="Target library input file" help="(-t) "/> + <param name="param_f" type="integer" min="1" max="2" optional="False" value="0" label="Fingerprint format [1 = binary bitstring, 2 = comma separated feature list]" help="(-f) "/> + <param name="param_fp_col" type="integer" value="-1" label="Column number for comma separated smiles input which contains the fingerprint" help="(-fp_col) "/> + <param name="param_id_col" type="integer" value="-1" label="Column number for comma separated smiles input which contains the molecule identifie" help="(-id_col) "/> + <param name="param_fp_tag" type="text" size="30" value=" " label="Tag name for SDF input which contains the fingerprint" help="(-fp_tag) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_id_tag" type="text" size="30" value=" " label="Tag name for SDF input which contains the molecule identifie" help="(-id_tag) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_tc" type="float" value="0.7" label="Tanimoto cutoff [default: 0.7]" help="(-tc) "/> + <param name="param_cc" type="integer" value="1000" label="Clustering size cutoff [default: 1000]" help="(-cc) "/> + <param name="param_l" type="integer" value="0" label="Number of fingerprints to read" help="(-l) "/> + <param name="param_nt" type="text" size="30" value="1" label="Number of parallel threads to use" help="(-nt) To use all possible threads enter <max> [default: 1]"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_sdf_out" type="integer" min="0" max="1" optional="True" value="0" label="If input file has SD format, this flag activates writing of clustering information as new tags in a copy of the input SD file" help="(-sdf_out) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Chemoinformatics]--> +<tool id="FingerprintSimilaritySearch" name="FingerprintSimilaritySearch" version="1.1.0"> + <description>calculate similar molecules in a library</description> + <macros> + <token name="@EXECUTABLE@">FingerprintSimilaritySearch</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_t" type="data" format="smi.gz,csv,sdf.gz,sdf,txt.gz,smi,txt,csv.gz" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="Target library input file" help="(-t) "/> + <param name="param_q" type="data" format="smi.gz,csv,sdf.gz,sdf,txt.gz,smi,txt,csv.gz" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="Query library input file" help="(-q) "/> + <param name="param_f" type="integer" min="1" max="2" optional="False" value="0" label="Fingerprint format [1 = binary bitstring, 2 = comma separated feature list]" help="(-f) "/> + <param name="param_fp_col" type="integer" value="-1" label="Column number for comma separated smiles input which contains the fingerprint" help="(-fp_col) "/> + <param name="param_id_col" type="integer" value="-1" label="Column number for comma separated smiles input which contains the molecule identifie" help="(-id_col) "/> + <param name="param_fp_tag" type="text" size="30" value=" " label="Tag name for SDF input which contains the fingerprint" help="(-fp_tag) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_id_tag" type="text" size="30" value=" " label="Tag name for SDF input which contains the molecule identifie" help="(-id_tag) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_tc" type="float" value="0.7" label="Tanimoto cutoff [default: 0.7]" help="(-tc) "/> + <param name="param_nt" type="text" size="30" value="1" label="Number of parallel threads to use" help="(-nt) To use all possible threads enter <max> [default: 1]"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_bs" type="integer" value="500" label="Block size [default: 500]" help="(-bs) "/> + <param name="param_sdf_out" type="integer" min="0" max="1" optional="True" value="0" label="If query file has SD format, this flag activates writing of nearest neighbours as a new CSV tag in a copy of the query SD file" help="(-sdf_out) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_t" format="input"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="GridBuilder" name="GridBuilder" version="1.1.0"> + <description>create score-grids for docking</description> + <macros> + <token name="@EXECUTABLE@">GridBuilder</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_pocket" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-pocket) "/> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_atom_types" type="text" size="30" value="C, H, N, O, P, S, Cl, F, I" label="elements for which grids should be precalculated" help="(-atom_types) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_grd" format="bngrd"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="IMGDock" name="IMGDock" version="1.1.0"> + <description>Iterative Multi-Greedy Docking</description> + <macros> + <token name="@EXECUTABLE@">IMGDock</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_pocket" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-pocket) "/> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="compounds to be docked" help="(-i) "/> + <param name="param_grd" type="data" format="bngrd,grd,grd.gz,bngrd.gz" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="ScoreGrid file" help="(-grd) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + <expand macro="advanced_options"> + <param name="param_IMGDock_superpose_ligand" type="boolean" truevalue="-IMGDock:superpose_ligand" falsevalue="" checked="true" optional="True" label="superpose ligands with ref.-ligand" help="(-superpose_ligand) "/> + <param name="param_IMGDock_decrease_stepwidth" type="boolean" truevalue="-IMGDock:decrease_stepwidth" falsevalue="" checked="false" optional="True" label="decrease step-width in each iterations" help="(-decrease_stepwidth) "/> + <param name="param_IMGDock_output_failed_dockings" type="boolean" truevalue="-IMGDock:output_failed_dockings" falsevalue="" checked="false" optional="True" label="output erroneous molecules" help="(-output_failed_dockings) "/> + <param name="param_IMGDock_iterations" type="integer" min="1" max="20" optional="True" value="4" label="max. IMG iterations" help="(-iterations) "/> + <param name="param_IMGDock_min_inhibitor_atoms" type="integer" min="0" max="100" optional="True" value="10" label="min. atoms in ref. lig. area" help="(-min_inhibitor_atoms) "/> + <param name="param_IMGDock_post_optimization_step_width" type="float" min="0.1" max="2.0" optional="True" value="0.5" label="translation opt. step-width" help="(-post_optimization_step_width) "/> + <param name="param_IMGDock_no_solutions" type="integer" min="10" max="1000" optional="True" value="100" label="num. multi-greedy solutions" help="(-no_solutions) "/> + <param name="param_IMGDock_post_optimization_steps" type="integer" min="0" max="10" optional="True" value="6" label="max. translation opt. steps" help="(-post_optimization_steps) "/> + <param name="param_IMGDock_step_width" type="integer" min="1" max="90" optional="True" value="10" label="step-width (bond angle discretization)" help="(-step_width) "/> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="InputPartitioner" name="InputPartitioner" version="1.1.0"> + <description>split QSAR data set </description> + <macros> + <token name="@EXECUTABLE@">InputPartitioner</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input data-file" help="(-i) "/> + <param name="param_n" type="integer" value="0" label="number of partitions" help="(-n) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="dat"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="InputReader" name="InputReader" version="1.1.0"> + <description>generate QSAR data set </description> + <macros> + <token name="@EXECUTABLE@">InputReader</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="sdf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input sd-file" help="(-i) "/> + <param name="param_act" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="sd-property containing response values" help="(-act) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_csv" type="data" format="csv" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input csv-file w/ additional descriptors" help="(-csv) "/> + <param name="param_csv_nr" type="integer" value="0" label="no. of response variables in csv-file" help="(-csv_nr) "/> + <param name="param_csv_sep" type="integer" value="0" label="separator symbol in csv-file" help="(-csv_sep) "/> + <param name="param_sdp" type="integer" min="0" max="1" optional="True" value="0" label="use sd-properties as additional descriptors" help="(-sdp) "/> + <param name="param_no_cd" type="integer" min="0" max="1" optional="True" value="0" label="do not center descriptors" help="(-no_cd) "/> + <param name="param_no_cr" type="integer" min="0" max="1" optional="True" value="0" label="do not center response values" help="(-no_cr) "/> + <param name="param_csv_cl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has compound (row) labels" help="(-csv_cl) "/> + <param name="param_csv_dl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has descriptor (column) labels" help="(-csv_dl) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="dat"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="InteractionConstraintDefiner" name="InteractionConstraintDefiner" version="1.1.0"> + <description>define interaction constraint</description> + <macros> + <token name="@EXECUTABLE@">InteractionConstraintDefiner</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_res" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="residue ID" help="(-res) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_s" type="float" value="0.0" label="desired minimal interation (score) between ligand and specified residue(s)" help="(-s) "/> + <param name="param_p" type="float" value="0.0" label="penalty value" help="(-p) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input configuration file" help="(-option) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="ini"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Checks and evaluations]--> +<tool id="LigCheck" name="LigCheck" version="1.1.0"> + <description>check molecules for errors</description> + <macros> + <token name="@EXECUTABLE@">LigCheck</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/> + <param name="param_ef" type="float" value="0.5" label="error fraction; print error if fraction of invalid mols is large" help="(-ef) "/> + <param name="param_ri" type="integer" min="0" max="1" optional="True" value="1" label="remove invalid molecules" help="(-ri) "/> + <param name="param_ut" type="integer" min="0" max="1" optional="True" value="0" label="check for unique topologies" help="(-ut) "/> + <param name="param_nc" type="integer" min="0" max="1" optional="True" value="0" label="no not check for unique conformations" help="(-nc) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="Ligand3DGenerator" name="Ligand3DGenerator" version="1.1.0"> + <description>generate 3D coordinates for small molecules</description> + <macros> + <token name="@EXECUTABLE@">Ligand3DGenerator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/> + <param name="param_ff" type="text" size="30" value="MMFF94" label="Forcefield to use for optimization (any available OpenBabel plugin)" help="(-ff) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + <param name="param_k" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates (flag precedes '-kp')" help="(-k) "/> + <param name="param_kp" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates but re-protonate compound in a pH dependent manner (flag is preceded by '-k')" help="(-kp) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="LigandFileSplitter" name="LigandFileSplitter" version="1.1.0"> + <description>split molecule files</description> + <macros> + <token name="@EXECUTABLE@">LigandFileSplitter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 + $token.param_o + #end if + #end for +#end if +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/> + <param name="param_no" type="integer" value="0" label="Number of output files to be created" help="(-no) "/> + <param name="param_mpf" type="integer" value="0" label="Number of molecules per output file" help="(-mpf) "/> + <param name="param_outname_pattern" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="Pattern that will be used to generate the names of the output files, see notes and examples below" help="(-outname_pattern) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>LigandFileSplitter splits a molecule file into a given number of subsets. + +Examples: + +$ 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. + + + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="ModelCreator" name="ModelCreator" version="1.1"> + <description>create a QSAR model </description> + <macros> + <token name="@EXECUTABLE@">ModelCreator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input dat-file" help="(-i) "/> + <param name="param_type" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="model type" help="(-type) "> + <option value="MLR">MLR</option> + <option value=" RR"> RR</option> + <option value=" PCR"> PCR</option> + <option value=" PLS"> PLS</option> + <option value=" OPLS"> OPLS</option> + <option value=" ALL"> ALL</option> + <option value=" KNN"> KNN</option> + <option value=" KPLS"> KPLS</option> + <option value=" KPCR"> KPCR</option> + <option value=" GP"> GP</option> + <option value=" SVR"> SVR</option> + <option value=" LDA"> LDA</option> + <option value=" snB"> snB</option> + <option value=" nB"> nB</option> + </param> + <param name="param_kernel" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="kernel type (in case of kernel-model)" help="(-kernel) "> + <option value="none">none</option> + <option value=" polynomial"> polynomial</option> + <option value=" rbf"> rbf</option> + <option value=" sigmoidal"> sigmoidal</option> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="mod"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="MolCombine" name="MolCombine" version="1.1.0"> + <description>combine molecular files</description> + <macros> + <token name="@EXECUTABLE@">MolCombine</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i1" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file A" help="(-i1) "/> + <param name="param_i2" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file B" help="(-i2) "/> + <param name="param_mode" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'intersection', 'union' or 'b_not_a'" help="(-mode) "> + <option value="intersection">intersection</option> + <option value=" union"> union</option> + <option value=" b_not_a"> b_not_a</option> + </param> + <param name="param_ignH" type="integer" min="0" max="1" optional="True" value="1" label="ignore hydrogens, i.e" help="(-ignH) match molecules to any protonation state"/> + <param name="param_replace_prop" type="integer" min="0" max="1" optional="True" value="0" label="replace properties from file 1 w/ those from file 2" help="(-replace_prop) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input files when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i1" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="MolDepict" name="MolDepict" version="1.1.0"> + <description>create structure diagrams</description> + <macros> + <token name="@EXECUTABLE@">MolDepict</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_max" type="integer" value="60" label="maximal number of pictures (default=60, 0=unlimited)" help="(-max) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdf"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="MolFilter" name="MolFilter" version="0.9"> + <description>filter molecule files </description> + <macros> + <token name="@EXECUTABLE@">MolFilter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule-file" help="(-i) "/> + <param name="param_min_logP" type="float" value="0.0" label="minimal logP value" help="(-min_logP) "/> + <param name="param_max_logP" type="float" value="20.0" label="maximal logP value" help="(-max_logP) "/> + <param name="param_min_MW" type="float" value="0.0" label="minimal molecular weight" help="(-min_MW) "/> + <param name="param_max_MW" type="float" value="10000000000.0" label="maximal molecular weight" help="(-max_MW) "/> + <param name="param_q" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="query molecules for similarity searching" help="(-q) "/> + <param name="param_min_sim" type="float" value="0.0" label="minimal average similarity" help="(-min_sim) "/> + <param name="param_max_sim" type="float" value="1.0" label="maximal similarity" help="(-max_sim) "/> + <param name="param_smarts" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_smarts_file" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts_file) "/> + <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not show progress information" help="(-quiet) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="MolPredictor" name="MolPredictor" version="1.1.0"> + <description>predict molecule activities with QSAR model</description> + <macros> + <token name="@EXECUTABLE@">MolPredictor</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="sdf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input sd-file" help="(-i) "/> + <param name="param_mod" type="data" format="mod" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="file containing QSAR model" help="(-mod) "/> + <param name="param_csv" type="data" format="csv" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input csv-file w/ additional descriptors" help="(-csv) "/> + <param name="param_csv_nr" type="integer" value="0" label="no. of response variables in csv-file" help="(-csv_nr) "/> + <param name="param_csv_sep" type="integer" value="0" label="separator symbol in csv-file" help="(-csv_sep) "/> + <param name="param_sdp" type="integer" min="0" max="1" optional="True" value="0" label="use sd-properties as additional descriptors" help="(-sdp) "/> + <param name="param_csv_cl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has compound (row) labels" help="(-csv_cl) "/> + <param name="param_csv_dl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has descriptor (column) labels" help="(-csv_dl) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input sd-file when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="sdf"/> + </outputs> + <help>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'. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="PDBCutter" name="PDBCutter" version="1.1.0"> + <description>separate ligand and receptor </description> + <macros> + <token name="@EXECUTABLE@">PDBCutter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i) "/> + <param name="param_lig_chain" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="chain-name of ligand" help="(-lig_chain) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_lig_name" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="ligand name" help="(-lig_name) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat name="rep_param_rm_ch" min="0" max="1" title="param_rm_ch"> + <param name="param_rm_ch" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="protein chains that are to be deleted" help="(-rm_ch) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <repeat name="rep_param_rm_res" min="0" max="1" title="param_rm_res"> + <param name="param_rm_res" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="pdb-residues that are to be deleted (" help="(-rm_res) e.g. water or ions)"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_rec" format="pdb"/> + <data name="param_lig" format="pdb"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Get Data]--> +<tool id="PDBDownload" name="PDBDownload" version="1.1.0"> + <description>retrieve pdb-file from pdb.org</description> + <macros> + <token name="@EXECUTABLE@">PDBDownload</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_id" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="PDB ID for desired structure" help="(-id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_p" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="proxy" help="(-p) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="PDBRMSDCalculator" name="PDBRMSDCalculator" version="1.1.0"> + <description>computes RMSD between protein poses </description> + <macros> + <token name="@EXECUTABLE@">PDBRMSDCalculator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i_pdb) "/> + <param name="param_i_query" type="data" format="dcd,txt,pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="molecule(s) to compare input file" help="(-i_query) "/> + <param name="param_i_type" type="select" optional="True" value="pdb" label="query type (pdb, dcd, or transformation file (rigid_transformations)" help="(-i_type) "> + <option value="pdb">pdb</option> + <option value=" dcd"> dcd</option> + <option value=" rigid_transformations"> rigid_transformations</option> + </param> + <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) "> + <option value="C_ALPHA">C_ALPHA</option> + <option value=" BACKBONE"> BACKBONE</option> + <option value=" ALL_ATOMS"> ALL_ATOMS</option> + </param> + <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) "> + <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option> + <option value=" RIGID_RMSD"> RIGID_RMSD</option> + <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="txt"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="PartialChargesCopy" name="PartialChargesCopy" version="1.1.0"> + <description>transfer part. charges between files</description> + <macros> + <token name="@EXECUTABLE@">PartialChargesCopy</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/> + <param name="param_chr" type="data" format="mol2,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="file containing the same molecules as the input file, but with (different) partial charges" help="(-chr) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_chr" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="PeptideBuilder" name="PeptideBuilder" version="1.1.0"> + <description>build a peptide </description> + <macros> + <token name="@EXECUTABLE@">PeptideBuilder</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>PeptideBuilder + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +</command> + <inputs> + <param name="param_i" type="data" format="txt" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input torsion-file" help="(-i) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>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 + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="PocketDetector" name="PocketDetector" version="1.1.0"> + <description>detect binding pocket</description> + <macros> + <token name="@EXECUTABLE@">PocketDetector</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input ini file" help="(-option) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="ini"/> + <data name="param_mol_out" metadata_source="param_rl" format="input"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="PoseIndices2PDB" name="PoseIndices2PDB" version="1.1.0"> + <description>converts pose indices into PDB files </description> + <macros> + <token name="@EXECUTABLE@">PoseIndices2PDB</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i_clust" type="data" format="txt" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input cluster index file" help="(-i_clust) "/> + <param name="param_i_trans" type="data" format="dcd" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input tranformation file" help="(-i_trans) "/> + <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input reference pdb file" help="(-i_pdb) "/> + <expand macro="advanced_options"> + <param name="param_o_id" type="text" size="30" value="$o.id" label="output file name prefix for 2nd to last pdb file" help="(-o_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last pdb file" help="(-o_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="Predictor" name="Predictor" version="1.1.0"> + <description>predict activities with QSAR model</description> + <macros> + <token name="@EXECUTABLE@">Predictor</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mod" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mod-file" help="(-i) "/> + <param name="param_dat" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="data-file containing prediction data set" help="(-dat) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="txt"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="PropertyModifier" name="PropertyModifier" version="1.1.0"> + <description>modify molecule property tags</description> + <macros> + <token name="@EXECUTABLE@">PropertyModifier</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_mode" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'delete', 'add' or 'rename' properties" help="(-mode) "> + <option value="add">add</option> + <option value=" rename"> rename</option> + <option value=" delete"> delete</option> + </param> + <param name="param_name" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="property name ('all' will erase all properties if in delete-mode)" help="(-name) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_value" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="property value (in case of prop. adding only)" help="(-value) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_new_name" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="new property name (in case of renaming only)" help="(-new_name) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Analysis]--> +<tool id="PropertyPlotter" name="PropertyPlotter" version="1.1.0"> + <description>plot molecule properties</description> + <macros> + <token name="@EXECUTABLE@">PropertyPlotter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_p1" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="name of property 1" help="(-p1) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_p2" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="name of property 2" help="(-p2) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="be quiet, i.e. do not print progress information" help="(-quiet) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="eps"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Checks and evaluations]--> +<tool id="ProteinCheck" name="ProteinCheck" version="1.1.0"> + <description>quality check for proteins structures</description> + <macros> + <token name="@EXECUTABLE@">ProteinCheck</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i) "/> + <param name="param_bc" type="integer" min="0" max="1" optional="True" value="0" label="ignore broken chains" help="(-bc) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdf"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="ProteinProtonator" name="ProteinProtonator" version="1.1.0"> + <description>protonate protein structures</description> + <macros> + <token name="@EXECUTABLE@">ProteinProtonator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Analysis]--> +<tool id="RMSDCalculator" name="RMSDCalculator" version="1.1.0"> + <description>calculate RMSD between ligand poses</description> + <macros> + <token name="@EXECUTABLE@">RMSDCalculator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/> + <param name="param_org" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="molecule file containing the original ('true') poses" help="(-org) "/> + <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not print progress information" help="(-quiet) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="RemoveWater" name="RemoveWater" version="1.1.0"> + <description>removes water from PDB file </description> + <macros> + <token name="@EXECUTABLE@">RemoveWater</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>RemoveWater + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +</command> + <inputs> + <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-i) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>This tool removes water from a given pdb file. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [ForceFields]--> +<tool id="ResidueChecker" name="ResidueChecker" version="1.1.0"> + <description>check residues to debug a protein structure wrt to PDB conventions</description> + <macros> + <token name="@EXECUTABLE@">ResidueChecker</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> + <param name="param_norm_names" type="integer" min="0" max="1" optional="True" value="0" label="ensures a consistent naming scheme for all atoms," help="(-norm_names) e.g. PDB conventions"/> + <param name="param_build_bonds" type="integer" min="0" max="1" optional="True" value="0" label="add missing bonds" help="(-build_bonds) "/> + <param name="param_frag_reconstruct" type="integer" min="0" max="1" optional="True" value="0" label="reconstruct incomplete fragments" help="(-frag_reconstruct) "/> + <param name="param_extra_atoms" type="integer" min="0" max="1" optional="True" value="0" label="check for extra atoms, i.e" help="(-extra_atoms) unknown in the reference fragment"/> + <param name="param_bond_length" type="integer" min="0" max="1" optional="True" value="0" label="check for invalid bond length" help="(-bond_length) "/> + <param name="param_int_net_charge" type="integer" min="0" max="1" optional="True" value="0" label="check if integer charges" help="(-int_net_charge) "/> + <param name="param_large_charges" type="integer" min="0" max="1" optional="True" value="0" label="check for too large charges" help="(-large_charges) "/> + <param name="param_large_net_charge" type="integer" min="0" max="1" optional="True" value="0" label="check for too large net charge" help="(-large_net_charge) "/> + <param name="param_overlapping_atoms" type="integer" min="0" max="1" optional="True" value="0" label="check for overlapptin atom positions" help="(-overlapping_atoms) "/> + <param name="param_nan_positions" type="integer" min="0" max="1" optional="True" value="0" label="check for ill-valued atomic positions" help="(-nan_positions) "/> + <param name="param_elements" type="integer" min="0" max="1" optional="True" value="0" label="check if atom names reflect the atomic element" help="(-elements) "/> + <param name="param_dublicate_atom_names" type="integer" min="0" max="1" optional="True" value="0" label="check for dublicated atom names" help="(-dublicate_atom_names) "/> + <param name="param_unknown_residues" type="integer" min="0" max="1" optional="True" value="0" label="check for unknown residues" help="(-unknown_residues) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>This tool checks the residues of a pdb file wrt. common inconsistencies such as missing atoms or suspicious distances. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Scoring]--> +<tool id="SLICK" name="SLICK" version="1.1.0"> + <description>scoring protein-carbohydrate interactions</description> + <macros> + <token name="@EXECUTABLE@">SLICK</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input receptor file" help="(-rec) "/> + <param name="param_lig" type="data" format="" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input ligand file" help="(-lig) "/> + <param name="param_cr" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="charge rules" help="(-cr) "/> + <param name="param_pr" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="radius rules for the polar solvation" help="(-pr) "/> + <param name="param_lj" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="use FILE for LJ parameters" help="(-lj) "/> + <param name="param_op" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="read options from FILE (command line overrides!)" help="(-op) "/> + <param name="param_v" type="integer" value="0" label="verbosity to level" help="(-v) "/> + <param name="param_s" type="float" value="0.0" label="scaling factor for receptor charges" help="(-s) "/> + <param name="param_t" type="float" value="0.0" label="scaling factor for ligand charges" help="(-t) "/> + <param name="param_E" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKEnergy" help="(-E) "/> + <param name="param_S" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKScore" help="(-S) "/> + <param name="param_u" type="integer" min="0" max="1" optional="True" value="0" label="unite atoms" help="(-u) "/> + <param name="param_n" type="integer" min="0" max="1" optional="True" value="0" label="read radius rules for the nonpolar solvation from FILE" help="(-n) "/> + <param name="param_N" type="integer" min="0" max="1" optional="True" value="0" label="scale nonpolar radii by FACTOR" help="(-N) "/> + <param name="param_log" type="integer" min="0" max="1" optional="True" value="0" label="write log file" help="(-log) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>This tool calculates the SLICKEnergy / SLICK Score for protein-carbohydrate complexes. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Analysis]--> +<tool id="ScoreAnalyzer" name="ScoreAnalyzer" version="1.1.0"> + <description>generate ROC or enrichment plots</description> + <macros> + <token name="@EXECUTABLE@">ScoreAnalyzer</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_mode" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'roc', 'top50', 'scatter' or 'enrichment'" help="(-mode) "> + <option value="roc">roc</option> + <option value=" top50"> top50</option> + <option value=" scatter"> scatter</option> + <option value=" enrichment"> enrichment</option> + </param> + <param name="param_title" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="plot title" help="(-title) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/> + <param name="param_s" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="score label" help="(-s) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_e" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="binding-free-energy/class label name" help="(-e) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_t" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="only in case of non-binary act" help="(-t) data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_b" type="integer" min="0" max="1" optional="True" value="0" label="binary experimental activity data" help="(-b) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="eps"/> + </outputs> + <help>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). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Preparation]--> +<tool id="SeperateMolecules" name="SeperateMolecules" version="1.1.0"> + <description>Split each multi molecule entry to separate single molecule entries</description> + <macros> + <token name="@EXECUTABLE@">SeperateMolecules</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="sdf,sd,mol2,mol" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file (mol mol2 sd sdf)" help="(-i) "/> + <param name="param_min_atoms" type="integer" value="0" label="only keep molecules having at least a minimal number of atoms" help="(-min_atoms) "/> + <param name="param_all" type="integer" min="0" max="1" optional="True" value="0" label="keep all contained molecules, but each in separated entries" help="(-all) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </outputs> + <help>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'). + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="SideChainGridBuilder" name="SideChainGridBuilder" version="1.1.0"> + <description>build side chain grid</description> + <macros> + <token name="@EXECUTABLE@">SideChainGridBuilder</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>SideChainGridBuilder + +#if $param_param: + -param $param_param +#end if +#if $param_d: + -d "$param_d" +#end if +</command> + <inputs> + <param name="param_param" type="data" format="ini" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="parameter file" help="(-param) "/> + <param name="param_d" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="output directory" help="(-d) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>This tool precalculates a side chain grid. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Analysis]--> +<tool id="SimilarityAnalyzer" name="SimilarityAnalyzer" version="0.9"> + <description>analyze similarity between molecule files</description> + <macros> + <token name="@EXECUTABLE@">SimilarityAnalyzer</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i1" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file 1" help="(-i1) "/> + <param name="param_i2" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file 2" help="(-i2) "/> + <param name="param_title" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="plot title" help="(-title) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not print status" help="(-quiet) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="pdf"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Rescoring]--> +<tool id="SimpleRescorer" name="SimpleRescorer" version="1.1.0"> + <description>rescore docking results</description> + <macros> + <token name="@EXECUTABLE@">SimpleRescorer</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="compounds to be rescored" help="(-i) "/> + <param name="param_function" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="scoring function: 'MM', 'PLP' or 'PB'" help="(-function) "> + <option value="MM">MM</option> + <option value=" PLP"> PLP</option> + <option value=" PB"> PB</option> + </param> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>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'. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="SpatialConstraintDefiner" name="SpatialConstraintDefiner" version="1.1.0"> + <description>define spatial constraint</description> + <macros> + <token name="@EXECUTABLE@">SpatialConstraintDefiner</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_option" type="data" format="ini" optional="True" value="0" label="input configuration file" help="(-option) "/> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/> + <param name="param_type" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="'fraction' or 'number' of compound atoms" help="(-type) "> + <option value="fraction">fraction</option> + <option value=" number"> number</option> + </param> + <param name="param_n" type="float" value="0.0" label="desired number/fraction of atoms in spatial area" help="(-n) "/> + <param name="param_p" type="float" value="0.0" label="penalty value" help="(-p) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="ini"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Rescoring]--> +<tool id="TaGResTrain" name="TaGResTrain" version="1.1.0"> + <description>Target-specific Grid-Rescoring, training</description> + <macros> + <token name="@EXECUTABLE@">TaGResTrain</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="training compound data set" help="(-i) "/> + <param name="param_method" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" help="(-method) "> + <option value="Rescoring3D">Rescoring3D</option> + <option value=" Rescoring4D"> Rescoring4D</option> + <option value=" Rescoring1D"> Rescoring1D</option> + </param> + <param name="param_function" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="scoring function: 'MM' or 'PLP'" help="(-function) "> + <option value="MM">MM</option> + <option value=" PLP"> PLP</option> + </param> + <param name="param_exp" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="property-tag name containing experimentally determined binding-free-energies" help="(-exp) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mod"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Rescoring]--> +<tool id="TaGRes" name="TaGRes" version="1.1.0"> + <description>Target-specific Grid-Rescoring</description> + <macros> + <token name="@EXECUTABLE@">TaGRes</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> + <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="compounds to be rescored" help="(-i) "/> + <param name="param_mod" type="data" format="mod" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="model-file generated by TaGRes-train" help="(-mod) "/> + <param name="param_tf" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="top-scored fraction of compounds not to be rescored" help="(-tf) "/> + <param name="param_method" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" help="(-method) "> + <option value="Rescoring3D">Rescoring3D</option> + <option value=" Rescoring4D"> Rescoring4D</option> + <option value=" Rescoring1D"> Rescoring1D</option> + </param> + <param name="param_function" type="select" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="scoring function: 'MM' or 'PLP'" help="(-function) "> + <option value="MM">MM</option> + <option value=" PLP"> PLP</option> + </param> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>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'. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="Trajectory2RigidTransformation" name="Trajectory2RigidTransformation" version="1.1.0"> + <description>converts a trajectory file into a rigid transformation file </description> + <macros> + <token name="@EXECUTABLE@">Trajectory2RigidTransformation</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i_dcd" type="data" format="dcd" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input trajectory file" help="(-i_dcd) "/> + <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i_pdb) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="txt"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Convert, combine and store]--> +<tool id="TrajectoryFile2PDBSplitter" name="TrajectoryFile2PDBSplitter" version="1.1.0"> + <description>splits SnapShots into PDB files </description> + <macros> + <token name="@EXECUTABLE@">TrajectoryFile2PDBSplitter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i_traj" type="data" format="dcd" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input trajectory file" help="(-i_traj) "/> + <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i_pdb) "/> + <expand macro="advanced_options"> + <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last pdb file" help="(-o_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [QuEasy (QSAR)]--> +<tool id="Validator" name="Validator" version="1.1.0"> + <description>evaluate quality of a QSAR model </description> + <macros> + <token name="@EXECUTABLE@">Validator</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_i" type="data" format="mod" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mod-file" help="(-i) "/> + <param name="param_dat" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="data-file" help="(-dat) "/> + <param name="param_type" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="feature-selection type" help="(-type) "> + <option value="cross validation">cross validation</option> + <option value=" bootstrapping"> bootstrapping</option> + <option value=" response permutation"> response permutation</option> + <option value=" evaluate fit to test data"> evaluate fit to test data</option> + </param> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" format="txt"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Docking]--> +<tool id="WaterFinder" name="WaterFinder" version="1.1.0"> + <description>find strongly bound waters </description> + <macros> + <token name="@EXECUTABLE@">WaterFinder</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +</command> + <inputs> + <param name="param_rec" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="receptor pdb-file" help="(-rec) "/> + <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="reference-ligand" help="(-rl) "/> + <param name="param_option" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="configuration file" help="(-option) "/> + <param name="param_wat" type="data" format="pdb" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file containing water molecules (if not part of rec.-file)" help="(-wat) "/> + <param name="param_ai" type="integer" min="0" max="1" optional="True" value="0" label="use ab-initio water search (ignore water in pdb-file), experimental!" help="(-ai) "/> + <expand macro="advanced_options"> + <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/> + <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/> + <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/> + <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/> + <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/> + <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/> + <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/> + <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/> + <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/> + <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/> + <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/> + <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/> + </expand> + </inputs> + <outputs> + <data name="param_o" format="pdb"/> + </outputs> + <help>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. + +</help> +</tool>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="gv" type="galaxy.datatypes.data:Text"/> + <datatype extension="ac" type="galaxy.datatypes.data:Text"/> + <datatype extension="drf.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="xyz" type="galaxy.datatypes.data:Text"/> + <datatype extension="grd.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="brk.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="mol.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="xyz.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="ini" type="galaxy.datatypes.data:Text"/> + <datatype extension="hin.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="bngrd.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="smi.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="sdf.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="ent.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="grd" type="galaxy.datatypes.data:Text"/> + <datatype extension="ent" type="galaxy.datatypes.data:Text"/> + <datatype extension="smi" type="galaxy.datatypes.data:Text"/> + <datatype extension="mol2.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="dcd" type="galaxy.datatypes.data:Text"/> + <datatype extension="txt.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="bngrd" type="galaxy.datatypes.data:Text"/> + <datatype extension="mol2" type="galaxy.datatypes.data:Text"/> + <datatype extension="pdb.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="dat" type="galaxy.datatypes.data:Text"/> + <datatype extension="sdf" type="galaxy.datatypes.data:Text"/> + <datatype extension="mol" type="galaxy.datatypes.data:Text"/> + <datatype extension="hin" type="galaxy.datatypes.data:Text"/> + <datatype extension="mod" type="galaxy.datatypes.data:Text"/> + <datatype extension="csv.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="brk" type="galaxy.datatypes.data:Text"/> + <datatype extension="eps" type="galaxy.datatypes.binary:Binary"/> + <datatype extension="ac.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip"/> + <datatype extension="sd" type="galaxy.datatypes.data:Text"/> + <datatype extension="pdb" type="galaxy.datatypes.data:Text"/> + <datatype extension="drf" type="galaxy.datatypes.data:Text"/> + </registration> +</datatypes>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros! + You can edit this file to add your own macros, if you so desire, or you can + add additional macro files using the m/macros parameter --> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="binary">@EXECUTABLE@</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="advanced_options"> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"/> + <when value="advanced"> + <yield/> + </when> + </conditional> + </xml> +</macros>
--- /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 @@ +<?xml version='1.0' encoding='UTF-8'?> +<toolbox> + <section id="section-id-Scoring" name="Scoring"> + <tool file="BALL/SLICK.xml"/> + </section> + <section id="section-id-Checksandevaluations" name="Checks and evaluations"> + <tool file="BALL/LigCheck.xml"/> + <tool file="BALL/ProteinCheck.xml"/> + </section> + <section id="section-id-Docking" name="Docking"> + <tool file="BALL/ConstraintsFinder.xml"/> + <tool file="BALL/DockPoseClustering.xml"/> + <tool file="BALL/ExtractClustersFromWardTree.xml"/> + <tool file="BALL/GridBuilder.xml"/> + <tool file="BALL/IMGDock.xml"/> + <tool file="BALL/InteractionConstraintDefiner.xml"/> + <tool file="BALL/PDBRMSDCalculator.xml"/> + <tool file="BALL/PocketDetector.xml"/> + <tool file="BALL/SideChainGridBuilder.xml"/> + <tool file="BALL/SpatialConstraintDefiner.xml"/> + <tool file="BALL/WaterFinder.xml"/> + </section> + <section id="section-id-ForceFields" name="ForceFields"> + <tool file="BALL/CalculateBindingFreeEnergy.xml"/> + <tool file="BALL/CalculateEnergy.xml"/> + <tool file="BALL/CalculateSolvationFreeEnergy.xml"/> + <tool file="BALL/ResidueChecker.xml"/> + </section> + <section id="section-id-StructureCreation" name="Structure Creation"> + <tool file="BALL/CrystalGenerator.xml"/> + </section> + <section id="section-id-GetData" name="Get Data"> + <tool file="BALL/CombiLibGenerator.xml"/> + <tool file="BALL/ExtractProteinSequence.xml"/> + <tool file="BALL/PDBDownload.xml"/> + </section> + <section id="section-id-Analysis" name="Analysis"> + <tool file="BALL/PropertyPlotter.xml"/> + <tool file="BALL/RMSDCalculator.xml"/> + <tool file="BALL/ScoreAnalyzer.xml"/> + <tool file="BALL/SimilarityAnalyzer.xml"/> + </section> + <section id="section-id-Preparation" name="Preparation"> + <tool file="BALL/AddMissingAtoms.xml"/> + <tool file="BALL/BindingDBCleaner.xml"/> + <tool file="BALL/BondOrderAssigner.xml"/> + <tool file="BALL/EvenSplit.xml"/> + <tool file="BALL/ExtractProteinChains.xml"/> + <tool file="BALL/Ligand3DGenerator.xml"/> + <tool file="BALL/LigandFileSplitter.xml"/> + <tool file="BALL/MolFilter.xml"/> + <tool file="BALL/PDBCutter.xml"/> + <tool file="BALL/PartialChargesCopy.xml"/> + <tool file="BALL/PeptideBuilder.xml"/> + <tool file="BALL/PropertyModifier.xml"/> + <tool file="BALL/ProteinProtonator.xml"/> + <tool file="BALL/RemoveWater.xml"/> + <tool file="BALL/SeparateMolecules.xml"/> + </section> + <section id="section-id-Convert,combineandstore" name="Convert, combine and store"> + <tool file="BALL/Converter.xml"/> + <tool file="BALL/DockResultMerger.xml"/> + <tool file="BALL/MolCombine.xml"/> + <tool file="BALL/MolDepict.xml"/> + <tool file="BALL/PoseIndices2PDB.xml"/> + <tool file="BALL/Trajectory2RigidTransformation.xml"/> + <tool file="BALL/TrajectoryFile2PDBSplitter.xml"/> + </section> + <section id="section-id-QuEasy(QSAR)" name="QuEasy (QSAR)"> + <tool file="BALL/AutoModel.xml"/> + <tool file="BALL/FeatureSelector.xml"/> + <tool file="BALL/InputPartitioner.xml"/> + <tool file="BALL/InputReader.xml"/> + <tool file="BALL/ModelCreator.xml"/> + <tool file="BALL/MolPredictor.xml"/> + <tool file="BALL/Predictor.xml"/> + <tool file="BALL/Validator.xml"/> + </section> + <section id="section-id-Chemoinformatics" name="Chemoinformatics"> + <tool file="BALL/FingerprintSimilarityClustering.xml"/> + <tool file="BALL/FingerprintSimilaritySearch.xml"/> + </section> + <section id="section-id-Rescoring" name="Rescoring"> + <tool file="BALL/AntitargetRescorer.xml"/> + <tool file="BALL/SimpleRescorer.xml"/> + <tool file="BALL/TaGRes-train.xml"/> + <tool file="BALL/TaGRes.xml"/> + </section> +</toolbox>