diff CADDSuite-1.0.1/galaxyconfigs/tools/DockResultMerger.xml @ 9:2cff9609f2c7

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/galaxyconfigs/tools/DockResultMerger.xml	Tue Nov 15 10:40:26 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="dockresultmerger" name="DockResultMerger" version="1.0.1">
+    <description>merge docking output files</description>
+    <command interpreter="bash"><![CDATA[../../DockResultMerger 
+#for $s in $series_i 
+   #if str( "${s.i.file_name}" ) != ''  and str( "${s.i.file_name}" ) != 'None' :
+      -i "${s.i.file_name}"
+   #end if
+#end for 
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $score ) != ''  and str( $score ) != 'None' :
+   -score "$score"
+#end if
+#if str( $min ) != ''  and str( $min ) != 'None' :
+   -min "$min"
+#end if
+#if str( $max ) != ''  and str( $max ) != 'None' :
+   -max "$max"
+#end if
+#if str( $k ) != ''  and str( $k ) != 'None' :
+   -k "$k"
+#end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <repeat name="series_i" title="input files" min="1">
+            <param name="i" optional="false" label="input files" type="data" format="mol2/sdf/drf"/>
+        </repeat>
+        <param name="score" optional="true" label="Optional: score property name" area="true" type="text" size="1x15" value="score"/>
+        <param name="min" optional="true" label="Optional: minimal score value" type="text" area="true" size="1x5" value=""/>
+        <param name="max" optional="true" label="Optional: maximal score value" type="text" area="true" size="1x5" value=""/>
+        <param name="k" optional="true" label="Optional: number of output molecules" type="text" area="true" size="1x5" value=""/>
+        <param name="rm" optional="true" label="remove input files after merging" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool merges and sorts molecule files as generated by docking or rescoring.
+
+You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
+
+ Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>
+</tool>
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