annotate galaxy_stubs/WaterFinder.xml @ 2:605370bc1def draft default tip

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<?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="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="reference-ligand" help="(-rl) "/>
    <param name="param_option" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="configuration file" help="(-option) "/>
    <param name="param_wat" type="data" format="pdb" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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>