<tool id="bih4maconda" name="Bih4MaConDa" version="0.1.4">
  <description>
	: Utility to detect potential contaminants in your peak list based on MaConDa database
  </description>
  <requirements>
  	<requirement type="package" version="0.6.3">perl-metabolomics-fragment-annotation</requirement>
  </requirements>
  <stdio>
      <exit_code range="1" level="fatal" />
  </stdio>
  
  <command><![CDATA[
         perl $__tool_directory__/bih4maconda.pl
         -input $variableMetadata_in
         -mzCol $colmass

         #if str($has_header.header_choice) == "YES":
          -header "${has_header.header}"
         #end if

         -ppmError $ppm_error
         -mode $mode
         -outputTab $outputTab
         -outputFull $outFull
         -verbose $verbose
  ]]></command>
  <inputs>
        <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" />
    
    	<conditional name="has_header">
    		<param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" />
        	<when value="YES">
        		<param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/>
        	</when>
        	<when value="NO"/>
    	</conditional>
    
    	<param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
        
      <param name="verbose" type="select" label="Verbose level" display="radio" help="">
	        <option value="1" selected="true">Low</option>
        	<option value="3" >High</option>
		  </param>
      

      <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/>

      <param name="mode" label="Molecular Species " type="select" display="radio" help="">
        <option value="POSITIVE">Positif Mode</option>
        <option value="NEGATIVE">Negatif Mode</option>
        <option value="NEUTRAL">Neutral Mass</option>
      </param> 

  </inputs>
  <outputs>
    <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA_Full.tabular" />
    <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA.tabular" />
  </outputs>
  <tests>
    <!--test 01 : short input id, mz and rt data -->
    <test>
      <param name="variableMetadata_in" value="in_test01_pos.tabular"/>
      <param name="header_choice" value="YES"/>
      <param name="header" value="1"/>
      <param name="colmass" value="2"/>
      <param name="ppm_error" value="5"/>
      <param name="mode" value="POSITIVE"/>
      <param name="verbose" value="3"/>
      <output name="outFull" file="outFull_test01.tabular"/>
      <output name="outputTab" file="outTab_test01.tabular"/>
    </test>
  </tests>
  <help><![CDATA[

.. class:: infomark

**Authors**
  | Franck Giacomoni - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) - based on the Perl CPAN package Metabolomics::Fragmentation::Annotation

---------------------------------------------------


======================
bih4MaDonDa
======================

-----------
Description
-----------

 | detection of potential contaminants in your peak list based on MaConDa database


Keywords
========

contaminants


-----------------
Workflow position
-----------------


.. image::
        :width: 800


-----------
Input files
-----------


+--------------------------------+-----------+
| Parameter : num + label        |  Format   |
+================================+===========+
| 1 : File with a list of masses |  tabular  |
+--------------------------------+-----------+

File of masses (Generally variable metadata file) must have at least the following column : 
    | Masses : column with all the masses in the tabular input file
    |


----------
Parameters
----------

File of masses
    | see "Input files" section above
    | Tabular file format, Generally variable metadata file
    | 

Do you have a header
    | YES (default) : parameter **Number of header lines** is visible
    | NO : all lines are considered to contain masses
    |

If 'have a header'='YES'

Number of header lines
    | Number of lines not containing masses values, these lines will be ignored
    |

In all header cases :

Column of Masses
    | Specify the column number for the mz in the tabular input file
    |


In all cases :

PPM error 
    | Specify a delta (in ppm) to apply on annotating mass - This value is a float.
    |


------------
Output files
------------

Two types of files (if you manually enter the masses both files are mingled):
    | BIH4MACONDA_(input.name)_FULL.tabular : for linking with others modules.
    | BIH4MACONDA_(input.name).tabular : an excel-like output will be available. 
    | 


---------------------------------------------------

---------------
Working example
---------------


.. class:: warningmark

Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
 | Format Data For Postprocessing
 | Perform LCMS Annotations

.. class:: warningmark

And their "W4M courses 2019":
 | Using Galaxy4Metabolomics - W4M table format for Galaxy
 | Annotation Banks - Annotation  
  
  ]]></help>
    <citations>
    <citation type="doi">10.1093/bioinformatics/bts527</citation>
  </citations>
</tool>