view METEXPtools/export_to_metexp_tabular.xml @ 25:9f03c8587d6b draft default tip

MetExp msclust upload format changed from tabular to csv

<tool id="export_to_metexp_tabular" 
    name="METEXP - Tabular file" 
    version="0.2.0">
  <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="csv" 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." >
           <validator type="empty_field" message="A value is required."></validator><!-- attribute optional="False" does not seem to work for params so validator is added -->
    </param>
            	
   <param name="tissue" type="text" size="80"
           label="Tissue(s) info"
           help="Metadata information to accompany the results when stored in MetExp DB."  >
           <validator type="empty_field" message="A value is required."></validator>
    </param>
           
   <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."  >
           <validator type="empty_field" message="A value is required."></validator>
    </param>
           
   <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."  >
           <validator type="empty_field" message="A value is required."></validator>
    </param>
                   
    <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."  >
           <validator type="empty_field" message="A value is required."></validator>
    </param>
    
  </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>