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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/galaxyconfigs/tools/TaGRes.xml	Tue Nov 15 10:53:16 2011 -0500
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+
+<!--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" name="TaGRes" version="1.0.1">
+    <description>Target-specific Grid-Rescoring</description>
+    <command interpreter="bash"><![CDATA[../../TaGRes 
+#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( $mod ) != ''  and str( $mod ) != 'None' :
+   -mod "$mod"
+#end if
+#if str( $tf ) != ''  and str( $tf ) != 'None' :
+   -tf "$tf"
+#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
+ | 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="compounds to be rescored" type="data" format="mol2/sdf/drf"/>
+        <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="mod"/>
+        <param name="tf" optional="true" label="Optional: top-scored fraction of compounds not to be rescored" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <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>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool rescores docking output poses using Target-specific Grid-Rescoring.
+Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool.
+As input TaGRes needs:
+
+    * 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.
+    * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
+
+TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy.
+
+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>
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