diff query_metexp.xml @ 21:19d8fd10248e

* Added interface to METEXP data store, including tool to fire queries in batch mode * Improved quantification output files of MsClust, a.o. sorting mass list based on intensity (last two columns of quantification files) * Added Molecular Mass calculation method

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/query_metexp.xml	Wed Mar 05 17:20:11 2014 +0100
@@ -0,0 +1,67 @@
+<tool id="query_metexp" 
+    name="METEXP - Query Database " 
+    version="0.1.0">
+  <description>Query a set of identifications against the METabolomics EXPlorer database</description>
+  <command interpreter="python">
+    query_metexp.py 
+    $input_file 
+    $casid_col
+    $formula_col 
+    $molecular_mass_col 
+    "$metexp_dblink_file"
+    $separation_method
+    $output_result 
+  </command>
+  <inputs>
+  
+   <param name="input_file" format="tabular" type="data" 
+        label="Input file"
+    	help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/>
+		
+   <param name="casid_col" type="text" size="50"
+           label="CAS ID column name"
+           value="CAS"
+           help="Name of the column containing the CAS code information (in the given input file)" /> 	
+   <param name="formula_col" type="text" size="50"
+           label="Formula ID column name"
+           value="FORMULA"
+           help="Name of the column containing the formula information (in the given input file)" /> 	
+   <param name="molecular_mass_col" type="text" size="50"
+           label="Molecular mass column name"
+           value="MM"
+           help="Name of the column containing the molecular mass information (in the given input file)" /> 	
+   
+   <param name="metexp_dblink_file" type="select" label="MetExp DB to query" 
+      		 help="Select the MetExp Database/backend which should be queried" 
+      		 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/>
+      		 
+  <param name="separation_method" type="select" label="Data type to query">
+  	<option value="GC" selected="True">GC</option>
+    <option value="LC">LC</option>
+  </param>    		     	
+    
+  </inputs>
+  <outputs>
+    <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" />
+  </outputs>
+  <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
+  <help>
+.. class:: infomark  
+  
+This tool will Query a set of identifications against the METabolomics EXPlorer database.
+
+It will take the input file and for each record it will query the 
+molecular mass in the selected MetExp DB. If one or more compounds are found in the
+MetExp DB then extra information regarding these compounds is added to the output file.
+
+The output file is thus the input file enriched with information about 
+related items found in the selected MetExp DB.  
+
+**Notes**
+
+The input file can be any tabular file, as long as it contains a column for the molecular mass
+and one for the formula of the respective identification.  
+  
+    
+  </help>
+</tool>