diff galaxy_stubs/SimpleRescorer.xml @ 2:605370bc1def draft default tip

Uploaded

--- /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="&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_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 rescored" help="(-i) "/>
+    <param name="param_function" type="select" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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>