--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml	Tue Jun 07 16:43:30 2011 -0400
@@ -0,0 +1,68 @@
+
+<!--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="inputreader" name="InputReader" version="1.1">
+    <description>generate QSAR data set</description>
+    <command interpreter="bash"><![CDATA[../../InputReader 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $act ) != ''  and str( $act ) != 'None' :
+   -act "$act"
+#end if
+#if str( $csv ) != ''  and str( $csv ) != 'None' :
+   -csv "$csv"
+#end if
+#if str( $csv_nr ) != ''  and str( $csv_nr ) != 'None' :
+   -csv_nr "$csv_nr"
+#end if
+#if str( $csv_sep ) != ''  and str( $csv_sep ) != 'None' :
+   -csv_sep "$csv_sep"
+#end if
+#if str( $sdp ) != ''  and str( $sdp ) != 'None' :
+   -sdp
+#end if
+#if str( $no_cd ) != ''  and str( $no_cd ) != 'None' :
+   -no_cd
+#end if
+#if str( $no_cr ) != ''  and str( $no_cr ) != 'None' :
+   -no_cr
+#end if
+#if str( $csv_cl ) != ''  and str( $csv_cl ) != 'None' :
+   -csv_cl
+#end if
+#if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
+   -csv_dl
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
+        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
+        <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/>
+        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="dat"/>
+    </outputs>
+    <help>This tool reads input from sd-files and generate features for QSAR analysis.
+Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
+The following number of features will be automatically created for each molecule in your sd-file:
+
+    * 40 atom and bond count descriptors
+    * 2 connectivity indices (Balaban and Zagreb index)
+    * 4 partial charge descriptors
+    * 14 surface descriptors
+    * 133 topological descriptors (functional group counts)
+
+If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
+Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help>
+</tool>
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