annotate galaxy_stubs/IMGDock.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="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="&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_pocket" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="compounds to be docked" help="(-i) "/>
    <param name="param_grd" type="data" format="bngrd,grd,grd.gz,bngrd.gz" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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>