view features_check_references.xml @ 1:c1008b92a6c8 draft

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<tool id="2021_05_features_check_references" name="Features -> checks references" version="0.0.1">

  <description>   </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("$__tool_directory__/src/mz_9_compares_peaks.sci",-1); ...
        lasterror(); ...
        ... //load "${peaks_list}"; ... // 22avril21
        peaks_list=glx_tab2div("${peaks_list}"); ...
        ...
        load "${peaks_detail}"; ...
        x836=glx_tab2div("${peaks_reference}"); ...
        diff_mz=${diff_mz}; ...
        k=${k}; ...
        x_peaks_final=mz_9_compares_peaks(peaks_list,peaks_detail,x836,diff_mz,k); ...
        ...
        div2tab(x_peaks_final,"${x_peaks_final}"); ... 
        if ~isempty(lasterror(%f)); ...
            write(0,lasterror()); ...
        end; ]]>
    </configfile>
  </configfiles>


  <inputs>
    <param name="peaks_list"      format="tabular"     type="data"      label="Features list"   help="from function  EIC->peaks:features"    />
    <param name="peaks_detail"    format="mat"     type="data"      label="Detailed features"     help="from function  EIC->peaks:features"  />
    <param name="peaks_reference" format="tabular" type="data"      label="Reference features"     help="2columns: mz and RT, with column and line headers" />
    <param name="diff_mz"         value="0.0050"   type="float"     label="Threshold for m/z values" />
    <param name="k"               value="1"        type="integer"   label="Number of extracted features for each reference feature"  help="the closest to the reference peak" />
   
  </inputs>
  
  
  <outputs>
    <data name="x_peaks_final"   format="tabular"  label="Identified features" />
  </outputs>
  
  
  <tests>
  
  <test>
       <param  name="peaks_list"          value="Peaks_list.tabular"/>
       <param  name="peaks_detail"        value="Peaks_details.mat"/>
       <param  name="peaks_reference"     value="ref_mz_rt.tab"/>
       <param  name="diff_mz"             value="0.0050"/>
       <param  name="k"                   value="1"/>
       <output name="x_peaks_final">
           <assert_contents> 
       	<has_text text="136.0616"/>
       	<has_text text="229.135"/>   
           </assert_contents>
       </output>
    </test>
    
  </tests>


<help>


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


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

==================================
FEATURES EXPERIMENTAL VS REFERENCE
==================================


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

This function checks reference features among experimental features. 

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

**Features list**

The tabular file yielded by the function: EICs -> peaks:features


**Detailed features**

The HDF5-scilab file yielded by the function: EICs -> peaks:features


**Reference features**

A tabular file containing 2 columns: m/z values then retention times

Row labels are the names of the reference features, e.g. chemical compounds



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

**Threshold for m/z values**

Observed features are associated to the reference features if 1) the difference in m/z values is under the threshold; 2) the reference RT falls within the range of the observed RTs.

Default: 0.0050

**Number of extracted features for each reference feature**

e.g. if the number is 2, the algorithm will extract the 2 experimental features closest to each reference feature.


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


**Identified features**

A tabular file with the columns: 

- name of the reference feature

- number of the reference feature in the input file: Reference features

- number of the experimental feature in the input files: Features List and Detailed features

- number of identifications= the number of reference features each experimental feature has been attributed to; target = 1 

- m/z value of the reference feature

- m/z value of the experimental feature 

- difference of m/z values

- RT of the reference feature

- RT of the experimental feature 

- difference of RT 

- signal of the experimental feature 


</help>


<citations>

</citations>


</tool>