annotate query_metexp.xml @ 49:f772a5caa86a

Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.

<tool id="query_metexp" 
    name="METEXP - Query Database " 
    version="0.1.0">
  <description>Query a set of identifications against the METabolomics EXPeriments 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="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"
           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")'/>
      		 

  </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>