# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1409408058 -7200
# Node ID 60b53f2aa48a3b750edc1ace9e590407ddf8c4c4
# Parent  0d534bce8e848a9bcc11b93134c9e4d5c3f037f4
Small fixes, added microminutes support to MsClust, removed TIC or MsClust output

diff -r 0d534bce8e84 -r 60b53f2aa48a MsClust.jar
Binary file MsClust.jar has changed
diff -r 0d534bce8e84 -r 60b53f2aa48a msclust.xml
--- a/msclust.xml	Fri May 09 17:11:11 2014 +0200
+++ b/msclust.xml	Sat Aug 30 16:14:18 2014 +0200
@@ -64,9 +64,7 @@
 	    
 	</command>
 	<inputs>
-	<!--  <param name="rankingWeightConfig" type="text" area="true" size="11x70" label="NB - TEST VERSION" 
-value="VERSION BEING TESTED AT THIS MOMENT...NOT READY FOR USE..."/>
-	-->
+
 	 	<param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />
 		<param name="dataType" type="select" size="30" label="Data type">
 				<option value="gcms"  selected="true">GC-MS</option>
@@ -222,6 +220,20 @@
 
 -----
 
+**Input**
+
+The input file should contain the following columns (in this order), followed by the sample intensity columns (one column with the
+intensity value for each sample):
+
+*ScanNR	
+*Ret(umin)	
+*Mass(uD)	
+*(Optional)retentionMean
+*(only required if retentionMean is present)retentionSD
+*N sample intensity columns...
+
+-----
+
 **Output**
 
 This tools returns a number of ouptut files and a small report. 
diff -r 0d534bce8e84 -r 60b53f2aa48a query_mass_repos.py
--- a/query_mass_repos.py	Fri May 09 17:11:11 2014 +0200
+++ b/query_mass_repos.py	Sat Aug 30 16:14:18 2014 +0200
@@ -276,7 +276,7 @@
     # Query data against repository :
     enriched_data = _query_and_add_data(input_data, molecular_mass_col, repository_dblink, error_margin, margin_unit)
     headers = input_data.keys() + ['SEARCH hits for ','SEARCH hits: db-names', 'SEARCH hits: molecular-formulas ',
-                                   'SEARCH hits: ids','SEARCH hits: descriptions', 'Link to SEARCH hits']
+                                   'SEARCH hits: ids','SEARCH hits: descriptions', 'Link to SEARCH hits']  #TODO - add min and max formula weigth columns
 
     _save_data(enriched_data, headers, output_result)
     
diff -r 0d534bce8e84 -r 60b53f2aa48a query_metexp.xml
--- a/query_metexp.xml	Fri May 09 17:11:11 2014 +0200
+++ b/query_metexp.xml	Sat Aug 30 16:14:18 2014 +0200
@@ -1,7 +1,7 @@
 <tool id="query_metexp" 
     name="METEXP - Query Database " 
     version="0.1.0">
-  <description>Query a set of identifications against the METabolomics EXPlorer database</description>
+  <description>Query a set of identifications against the METabolomics EXPeriments database</description>
   <command interpreter="python">
     query_metexp.py 
     $input_file 
@@ -18,6 +18,12 @@
         label="Input file"
     	help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/>
 		
+  <param name="separation_method" type="select" label="Data type to query">
+  	<option value="GC" selected="True">GC</option>
+    <option value="LC">LC</option>
+  </param>    		     	
+    	
+		
    <param name="casid_col" type="text" size="50"
            label="CAS ID column name"
            value="CAS"
@@ -35,11 +41,7 @@
       		 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}" />
diff -r 0d534bce8e84 -r 60b53f2aa48a test/test_library_lookup.py
--- a/test/test_library_lookup.py	Fri May 09 17:11:11 2014 +0200
+++ b/test/test_library_lookup.py	Sat Aug 30 16:14:18 2014 +0200
@@ -149,7 +149,7 @@
         '''
         riqc_libs_dir = resource_filename(__name__, "../repositories/PRIMS-metabolomics/RI_DB_libraries")
         get_library_files_output = match_library.get_directory_files(riqc_libs_dir)
-        self.assertEqual(1, len(get_library_files_output))
+        self.assertEqual(2, len(get_library_files_output))
         self.assertEqual("Library_RI_DB_capillary_columns-noDuplicates", get_library_files_output[0][0])
         #TODO change assert below to assert that the result is a file, so the test can run on other dirs as well:
         #self.assertEqual("E:\\workspace\\PRIMS-metabolomics\\python-tools\\tools\\GCMS\\test\\data\\riqc_libs\\RI DB library (capillary columns) Dec.2012.txt", get_library_files_output[0][1])