diff CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml @ 3:bb26168c5715

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--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="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95">
+    <description>define spatial constraint</description>
+    <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
+#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( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select">
+            <option value="fraction">fraction</option>
+            <option value="number">number</option>
+        </param>
+        <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/>
+        <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="1e11"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool allows to define spatial constraints for docking or scoring.
+
+For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
+Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
+
+Output of this tool is a ini-file that contains the desired spatial constraint.</help>
+</tool>
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