--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GCMS/library_lookup.xml	Thu Mar 19 12:22:23 2015 +0100
@@ -0,0 +1,75 @@
+<tool id="lookup_library" name="RIQC-Lookup RI for CAS numbers in library" version="1.0.2">
+  <description>Lookup or estimate the RI using a "known RI values" CAS numbers library</description>
+  <command interpreter="python">
+    library_lookup.py 
+    $library_file
+    $input 
+    "$col_type" 
+    "$polarity" 
+    $output
+    #for $ctype in $pref
+      ${ctype.columntype}
+    #end for
+    $regression.model	
+  </command>
+  <inputs>
+  <!-- Regarding the <page> items: this blocks the use of this tool in Galaxy workflows. However, 
+       alternatives like wrapping this in conditionals, repeats (to force a refresh_on_change as this option 
+       is not working on its own) failed since the workflow editor does not support refreshes...not does the 
+       workflow runtime support conditionals or repeats to be set at runtime. See also 
+       galaxy-dev mail thread "when else" in <conditional> ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??"  -->
+    <page>
+      <param format="tabular" name="input" type="data" label="NIST identifications as tabular file" 
+      		 help="Select a tab delimited NIST metabolite identifications file (converted from PDF)" />
+      <param name="library_file" type="select" label="CAS x RI Library file" 
+      		 help="Select a library/lookup file containing RI values for CAS numbers on various chromatography columns " 
+      		 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/RI_DB_libraries")'/>
+    </page>
+    <page>
+      <param name="col_type" type="select" label="Select column type" refresh_on_change="true"
+	         display="radio" dynamic_options='get_column_type(library_file)'
+	         help="" />
+	</page>
+    <page>
+      <param name="polarity" type="select" label="Select polarity" refresh_on_change="true"
+             display="radio" dynamic_options='filter_column(library_file,col_type)'
+	         help="" />
+    </page>
+    <page>
+	  <conditional name="regression">
+		  <param name="regression_select" type="boolean" checked="false" label="Apply regression method" 
+		  		 help="If no data for the selected column is present in the database, selecting this option will try 
+		  		 	   to convert Retention Indices using data from other GC-columns with a regression method. Please
+		  		 	   note that only the first given GC-column above will be used for this, any alternatives will be
+		  		 	   ignored" />
+		  <when value="true">
+		  	<param name="model" format="tabular" type="data" label="Tabular file containing regression model" 
+		  		   help="This file contains the coefficients used to perform the regression from one GC-column
+		  		         to another GC-column"/>     
+		  </when>
+          <when value="false">
+            <param name="model" type="hidden" value="False" />
+          </when>
+	  </conditional>
+      <repeat name="pref" title="Select column name preference">
+		<param name="columntype" type="select" label="Column name" refresh_on_change="true"
+               dynamic_options='filter_column2(library_file, col_type, polarity)'
+	       	   help="Select one or more column names for filtering. The order defines the priority." />
+      </repeat>
+    </page>
+  </inputs>
+  <outputs>
+    <data format="tabular" label="${tool.name} on" name="output" />
+</outputs>
+<code file="match_library.py" />
+  <help>
+Performs a lookup of the RI values by matching CAS numbers from the given NIST identifications file to a library.
+If a direct match is NOT found for the preferred column name, a regression can be done to find
+the theoretical RI value based on known RI values for the CAS number on other column types (see step 4).
+If there is no match for the CAS number on any column type, then the record is not given a RI. 
+
+
+
+  </help>
+
+</tool>