view eics_merged.xml @ 5:e2541ea9c53c draft default tip

Uploaded

<tool id="2021_05_eics_merged" name="EICs-synchronized -> EICs-merged" 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("$__tool_directory__/src/mz_8_merge_list_x_tr_mz4.sci",-1); ...
      lasterror(); ...
      load("${list_eic4_files}");  ...  // the variable name is also: list_eic4_files
      [x_tr_mz4,ppm_coupe]=mz_8_merge_list_x_tr_mz4(list_eic4_files); ...
      div2tab(x_tr_mz4,"${merged_x_tr_mz4file}"); ...
      if ~isempty(lasterror(%f)) then ...
        write(0,lasterror()); ...
      end; ]]>
    </configfile>
  </configfiles>


  <inputs>
    <param name="list_eic4_files"  format="mat"  type="data" label="Select X data" help="a list of EIC-synchronized files with all the same mz values "/>
  </inputs>


  <outputs>
    <data name="merged_x_tr_mz4file" format="tabular"  label="EICs-merged"/>
  </outputs>
  
  
  <tests>
  
    <test>
       <param  name="list_eic4_files"       value="EICs-synchronized.mat"/>
       <output name="merged_x_tr_mz4file"   file="EICs-merged.tab" compare="sim_size" delta="1000" />
    </test>
    
  </tests>
  
<help>


.. class:: infomark

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


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

==========================
MEAN OF SEVERAL EICS FILES
==========================

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

Several EIC files correspond to the same sample (e.g. repetitions). They share the same m/z values, not necessary the same retention times even if their RTi should be close.

This function merges them into a single (RT x m/z) dataset


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

**Select Xdata**

At least two datasets, gathered into a single HDF5-scilab .dat file issued from the function: EICs-individual - EICs-synchronized

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

**EICs-merged**

The merged EICs in a tabular file.


</help>


<citations>

</citations>

</tool>