view eics_check_references.xml @ 2:cfcdd499c781 draft

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<tool id="2021_05_eics_check_references" name="EICs -> checks reference mz" version="0.0.1">
  
  <description> for 5 determined thresholds for m/z  </description>
 
  <requirements>
      <requirement type="package">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("$__tool_directory__/src/mz_0_publi_features4_galaxy.sci",-1); ...
        exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
        lasterror(); ...
        ...
        x_in=glx_tab2div("${xtrmz4}"); ...  // 20avril21
        [x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}",x_in, ${electron}); ...
        ... //[x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}", "${xtrmz4}", ${electron}); ...
        ...
        div2tab(x_bilan, "${xbilan}"); ...
        save("${xsynthese}","x_synthese"); ...
        save("${x_tr_mz_trouves}","x_tr_mz4"); ...
        if ~isempty(lasterror(%f)); ...
        write(0,lasterror()); ...
        end; ]]>
    </configfile>
  </configfiles>

 
  <inputs>
    <param name="mzref"       format="tabular"            type="data"      label="Reference m/z values"    />
    <param name="xtrmz4"      format="tabular"            type="data"      label="EICs-mean"    />
    <param name="electron"    size="5"       value="0"    type="integer"   label="Electron mass" help="1=correction of the reference m/z values; 0=no correction"    />
  </inputs>


  <outputs>
    <data name="xbilan"           format="tabular"      label="m/z check-summary"  />
    <data name="xsynthese"        format="mat"          label="m/z check-details"  />
    <data name="x_tr_mz_trouves"  format="mat"          label="m/z check-matrix"   />
  </outputs>
  
  
  <tests>
  
    <test>
       <param  name="mzref"                 value="ref_mz.tab"/>
       <param  name="xtrmz4"                value="EICs-merged.tab"/>
       <output name="xbilan">
           <assert_contents> 
       	<has_text text="0.00034"/>
       	<has_text text="0.352"/>   
           </assert_contents>
       </output>
    </test>
    
  </tests>
<help>


**Author**  Jean-Claude Boulet (INRA).


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

=======================================================================
CHECK REFERENCE MZ VALUES AMONG THE EICS-MEAN YIELDED BY THE PROCESSING
=======================================================================

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

A matrix of EICs has been yielded by the function: MS-centroid -> EICs-individual or by the function: several EICs-shared -> one EICs-mean.

The m/z values of these EICs are compared to reference m/z values for 5 pre-determined threshold values for m/z: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100. 

This function is focused on the m/z values, it does not take into account the retention times. 



------
Inputs
------

**reference m/z values**

A tabular file, to the div format (first columns and rows = labels):

- the first column corresponds to names of chemical compounds;

- the second column contains the exact (reference) m/z values.


**EICs-mean or individual**

A tabular matrix of (RT x m/z); lines are retention times and columns are EICs.


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

**correction of the electron mass**

A correction can be applied to the reference m/z values. 

- 0: no correction;

- 1: correction = subtraction of 0.00055 in the positive mode. 



------
Output
------

**summary**

The main results  


**details**

A .mat file


**extracted EICs**

An EIC is associated to a reference m/z value if the absolute difference of (EIC minus reference) is under a threshold. 

Five threshold values have been pre-determined: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100

This output contains a list of 5 data, each containing the EICs identified as reference m/z values according to a threshold. 

</help>


<citations>

</citations>


</tool>