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<tool id="2021_05_eics_synchronization" name="EICs-individual -> EICs-synchronized" version="0.0.1">

  <description>  for a series of close mass spectra, e.g. repetitions  </description>
  
  
  <requirements>
      <requirement type="package" version="6.0.2">scilab</requirement>
  </requirements>
  
  
  <stdio>
      <exit_code range="1:" level="fatal" />
  </stdio>
  
  
  <command> 
   <![CDATA[ 
    $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file}  
    ]]>
  </command>
  
  
  <configfiles>
    <configfile name="script_file">
      <![CDATA[ exec("$__tool_directory__/src/mz_4_extract_final_mz_v3.sci",-1); ...
      lasterror(); ...
      col=list(); ...
      #for $i, $s in enumerate( $series )
        x_tr_mz3=glx_tab2div("${s.Xdata.file_name}"); ...
        ... //  load("${s.Xdata.file_name}"); ...  22avril21
        x${i}=x_tr_mz3; ...
        col(${i}+1)=x${i}; ...
      #end for
      ...
      [list_eic4_files,mz4_stats]=mz_4_extract_final_mz_v3(col,${delta_mz}); ...
      save("${list_eic4_files}",'list_eic4_files'); ...
      save("${mz4_stats}",'mz4_stats'); ...
      if ~isempty(lasterror(%f)) then ...
        write(0,lasterror()); ...
      end; ]]> 
    </configfile>
  </configfiles>


  <inputs>
    <repeat    name="series"    title="dataset" min="2">
        <param name="Xdata"     format="tabular"    type="data"  label="Input file"  help="EICs-individual files"/>
    </repeat>
    <param     name="delta_mz"  value="0.0024"  type="float" label="Threshold for m/z"  />
  </inputs>


  <outputs>
    <data name="list_eic4_files" format="mat"   label="EICs-synchronized"/>
    <data name="mz4_stats"       format="mat"   label="stats on EIC-synchro"/>
  </outputs>


  <tests>

     <test>
       <param name="Xdata" value="EICs-individual-1_k3mean.tab"/>
       <param name="Xdata" value="EICs-individual-2_k3mean.tab"/>
       <param name="Xdata" value="EICs-individual-3_k3mean.tab"/>
       <param name="delta_mz"     value="0.0024"/>
       <output name="list_eic4_files"   file="EICs-synchronized.mat" compare="sim_size" delta="1000" />
    </test>
    
  </tests>


<help>


.. class:: infomark

**Author** Jean-Claude Boulet (INRAE)


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

=================================================
EXTRACTS THE EICS SHARED BY A SERIES OF EIC FILES
=================================================

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

The EICs shared by a series of EICs-individual are identified. 

Then, each of the initial EiCs-individual is reprocessed as to keep only the EICs shared by all the series.  

The main application is the synchronization of the EICs of repetitions.



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

At least two EICs-individual

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

**Threshold for m/z**

Two m/z values whose difference is larger than this threshold will be considered as different. 

Default value: 0.0024


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


**EICs-shared**

The input files with the same EICs. 

A list at the HDF5-scilab .dat format. 



**stats on EICs-shared**

Some calculations for the following processings. 

</help>


<citations>

</citations>

</tool>