diff CADDSuite/galaxyconfigs/tools/TaGRes-train.xml @ 5:b7a89b15646f

Uploaded

--- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="tagres-train" name="TaGRes-train" version="0.94">
+<tool id="tagres-train" name="TaGRes-train" version="0.95">
     <description>Target-specific Grid-Rescoring, training</description>
     <command interpreter="bash"><![CDATA[../../TaGRes-train 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -30,20 +30,20 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="training compound data set" type="data" format="mol2/sdf/drf"/>
+        <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select">
             <option value="Rescoring3D">Rescoring3D</option>
             <option value="Rescoring4D">Rescoring4D</option>
             <option value="Rescoring1D">Rescoring1D</option>
         </param>
-        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+        <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select">
             <option value="MM">MM</option>
             <option value="PLP">PLP</option>
         </param>
-        <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="exp" optional="false" label="property-tag name containing experimentally determined binding-free-energies" area="true" type="text" size="1x15" value="binding_free_energy"/>
     </inputs>
     <outputs>
         <data name="o" format="mod"/>
@@ -55,7 +55,7 @@
     * 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 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.
+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 this 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>
+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>
\ No newline at end of file