annotate query_mass_repos.xml @ 60:35f506f30ae4

fixed small rule in pdfread, and other small enhancements

<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>