diff CADDSuite-1.6/galaxyconfigs/tools/WaterFinder.xml @ 10:eda78e0f5df6 draft default tip

Deleted selected files

--- a/CADDSuite-1.6/galaxyconfigs/tools/WaterFinder.xml	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-
-<!--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="waterfinder" name="WaterFinder" version="1.6">
-    <description>find strongly bound waters</description>
-    <command interpreter="bash"><![CDATA[../../WaterFinder 
-#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( $wat ) != ''  and str( $wat ) != 'None' :
-   -wat "$wat"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ai ) != ''  and str( $ai ) != 'None' :
-   -ai
-#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="wat" optional="true" label="input pdb-file containing water molecules (if not part of rec.-file)" type="data" format="pdb"/>
-        <param name="ai" optional="true" label="use ab-initio water search (ignore water in pdb-file), experimental!" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdb"/>
-    </outputs>
-    <help>This tool searches for crystal waters that
-    * either interact very strongly with the receptor
-    * or that interact strongly with receptor and reference ligand, 
-      thus functioning as a water bridge.
-
-Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
-
-As input we need:
-    * a file containing a protonated protein in pdb-format.
-      This file should contain water molecules that are to be evaluated by this tool.
-      However, you can also use a separate pdb-file as input for the water molecules (see below).
-    * 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).
-    * optionally a file in pdb-format containing water molecules.
-      If you specify such a file , all water molecules appearing in the
-      protein input-file (if any) will be ignored.
-
-Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help>
-</tool>
\ No newline at end of file