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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/galaxyconfigs/tools/ConstraintsFinder.xml	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,38 @@
+
+<!--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="constraintsfinder" name="ConstraintsFinder" version="1.0.1">
+    <description>find strongly interacting residues</description>
+    <command interpreter="bash"><![CDATA[../../ConstraintsFinder 
+#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( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#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"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool searches protein residues with which the reference ligand interacts strongly.
+Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
+
+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).
+
+Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.</help>
+</tool>
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