--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/query_mass_repos.xml	Sat Feb 07 22:02:00 2015 +0100
@@ -0,0 +1,106 @@
+<tool id="query_mass_repos" 
+    name="METEXP - Find elemental composition formulas based on mass values " 
+    version="0.1.0">
+  <description>Query multiple public repositories for elemental compositions from accurate mass values detected by high-resolution mass spectrometers</description>
+  <command interpreter="python">
+    query_mass_repos.py 
+    $input_file 
+    "$molecular_mass_col"
+    "$repository_file"
+    $error_margin
+    $margin_unit
+    $output_result 
+  </command>
+  <inputs>
+  
+   <param name="input_file" format="tabular" type="data" 
+        label="Input file"
+    	help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/>
+		
+   <param name="molecular_mass_col" type="text" size="50"
+           label="Molecular mass column name"
+           value="MM"
+           help="Name of the column containing the molecular mass information (in the given input file)" /> 	
+   
+   <param name="repository_file" type="select" label="Repository/service to query" 
+      		 help="Select the repository/service which should be queried" 
+      		 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_MassSearch_Services")'/>
+      		 
+   <param name="error_margin" type="float" size="10"
+           label="Error marging"
+           value="0.01"
+           help="Mass difference allowed when searching in the repositories for a mass match." /> 
+   
+   <param name="margin_unit" type="select" label="Margin unit">
+	  	<option value="ms" selected="True">ms</option>
+	    <option value="ppm">ppm</option>
+   </param>         
+   <!-- TODO 
+   <param name="metexp_access_key" type="text" size="50"
+           label="(Optional)MetExp access key"
+           value=""
+           help="Key needed to get access to MetExp services. Fill in if MetExp service was selected" />    -->    	
+    
+  </inputs>
+  <outputs>
+    <data name="output_result" format="tabular" label="${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 multiple public repositories such as PRI-MetExp or http://webs2.kazusa.or.jp/mfsearcher 
+for elemental compositions from accurate mass values detected by high-resolution mass spectrometers.
+
+It will take the input file and for each record it will query the 
+molecular mass in the selected repository. If one or more compounds are found in the
+repository then extra information regarding (mass based)matching elemental composition formulas is added to the output file.
+
+The output file is thus the input file enriched with information about 
+related items found in the selected repository.  
+
+**Notes**
+
+The input file can be any tabular file, as long as it contains a column for the molecular mass.  
+
+**Services that can be queried**
+
+================= =========================================================================
+Database          Description
+----------------- -------------------------------------------------------------------------
+PRI-MetExp        LC-MS and GC-MS data from experiments from the metabolomics group at 
+                  Plant Research International. NB: restricted access to employees with 
+                  access key.    
+ExactMassDB       A database of possible elemental compositions consits of C: 100, 
+                  H: 200, O: 50, N: 10, P: 10, and S: 10, that satisfy the Senior and 
+                  the Lewis valence rules.  
+                  (via /mfsearcher/exmassdb/)
+ExactMassDB-HR2   HR2, which is one of the fastest tools for calculation of elemental 
+                  compositions, filters some elemental compositions according to 
+                  the Seven Golden Rules (Kind and Fiehn, 2007). The ExactMassDB-HR2 
+                  database returns the same result as does HR2 with the same atom kind 
+                  and number condition as that used in construction of the ExactMassDB.  
+                  (via /mfsearcher/exmassdb-hr2/)
+Pep1000           A database of possible linear polypeptides that are 
+                  constructed with 20 kinds of amino acids and having molecular 
+                  weights smaller than 1000.  
+                  (via /mfsearcher/pep1000/)
+KEGG              Re-calculated compound data from KEGG. Weekly updated.  
+                  (via /mfsearcher/kegg/)
+KNApSAcK          Re-calculated compound data from KNApSAcK.  
+                  (via /mfsearcher/knapsack/)
+Flavonoid Viewer  Re-calculated compound data from Flavonoid Viewer .  
+                  (via /mfsearcher/flavonoidviewer/
+LipidMAPS         Re-calculated compound data from LIPID MAPS.  
+                  (via /mfsearcher/lipidmaps/)
+HMDB              Re-calculated compound data from Human Metabolome Database (HMDB) 
+                  Version 3.5.  
+                  (via /mfsearcher/hmdb/)
+PubChem           Re-calculated compound data from PubChem. Monthly updated.  
+                  (via /mfsearcher/pubchem/)
+================= =========================================================================
+  
+Sources for table above: PRI-MetExp and http://webs2.kazusa.or.jp/mfsearcher 
+    
+  </help>
+</tool>