diff export_to_metexp_tabular.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/export_to_metexp_tabular.xml	Wed Mar 05 17:20:11 2014 +0100
@@ -0,0 +1,57 @@
+<tool id="export_to_metexp_tabular" 
+    name="METEXP - Tabular file" 
+    version="0.1.0">
+  <description>Create tabular file for loading into METabolomics EXPlorer database</description>
+  <command interpreter="python">
+    export_to_metexp_tabular.py $rankfilter_and_caslookup_combi $msclust_quant_file $output_result 
+    $organism $tissue $experiment_name $user_name $column_type
+  </command>
+  <inputs>
+    <param format="tabular" name="rankfilter_and_caslookup_combi" type="data" label="RIQC-Combine RankFilter and CasLookup output"
+    	help="Select the (multi) output file from the 'Combine RankFilter and CasLookup' tool"/>
+    <param format="tabular" name="msclust_quant_file" type="data" label="MusClust-quantification file output" 
+    	help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/>
+    	
+    	
+   <param name="organism" type="text" size="80"
+           label="Organism(s) info"
+           help="Metadata information to accompany the results when stored in MetExp DB." /> 	
+   <param name="tissue" type="text" size="80"
+           label="Tissue(s) info"
+           help="Metadata information to accompany the results when stored in MetExp DB." />
+           
+   <param name="experiment_name" type="text" size="80"
+           label="Experiment name/code"
+           help="Name or code to store the results under. This can help you find the results back in MetExpDB." />  
+           
+   <param name="user_name" type="text" size="80"
+           label="User name"
+           help="User name or code to store the results under. This can help you find the results back in MetExpDB." />  
+                   
+    <param name="column_type" type="text" size="80"
+           label="Column type"
+           help="Column type to report with the results. This can help you find the results back in MetExpDB." />    
+    
+  </inputs>
+  <outputs>
+    <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" />
+  </outputs>
+  <help>
+.. class:: infomark  
+  
+Tool to combine output from the tools RankFilter, CasLookup and MsClust
+into a tabular file that can be uploaded to the METabolomics EXPlorer (MetExp) database.
+
+RankFilter, CasLookup are already combined by 'RIQC-Combine RankFilter and CasLookup' tool so here we will use
+this result. 
+
+**Notes**
+
+Extra calculations performed:
+- The columns MM and MW are also added here and are derived from the column FORMULA found in RankFilter, CasLookup combined result. 
+  
+So in total here we merge 2 files and calculate one new column. 
+  
+    
+  </help>
+</tool>