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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/galaxyconfigs/tools/SimpleRescorer.xml	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,49 @@
+
+<!--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="simplerescorer" name="SimpleRescorer" version="1.0.1">
+    <description>rescore docking results</description>
+    <command interpreter="bash"><![CDATA[../../SimpleRescorer 
+#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( $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="function" optional="true" label="scoring function: 'MM', 'PLP' or 'PB'" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+            <option value="PB">PB</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </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>
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