Mercurial > repos > luis > ball
diff galaxy_stubs/WaterFinder.xml @ 2:605370bc1def draft default tip
Uploaded
author | luis |
---|---|
date | Tue, 12 Jul 2016 12:33:33 -0400 |
parents | |
children |
line wrap: on
line diff
--- /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>