diff CADDSuite-1.0.1/galaxyconfigs/tools/TaGRes-train.xml @ 5:e30a41af9d2b

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/galaxyconfigs/tools/TaGRes-train.xml	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,61 @@
+
+<!--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="1.0.1">
+    <description>Target-specific Grid-Rescoring, training</description>
+    <command interpreter="bash"><![CDATA[../../TaGRes-train 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $method ) != ''  and str( $method ) != 'None' :
+   -method "$method"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+#if str( $exp ) != ''  and str( $exp ) != 'None' :
+   -exp "$exp"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <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" optional="true" label="scoring function: 'MM' or 'PLP'" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+        </param>
+        <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"/>
+    </outputs>
+    <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
+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 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 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 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>
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