view 2018_07_mz_hdf5_to_dat.xml @ 0:4082283be00c draft

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<tool id="2021_05_hdf5_to_dat" name="MS .h5 -> MS .dat " version="0.0.1">

<description> from an Orbitrap MS  </description>
 

<requirements>
    <requirement type="package" >scilab</requirement>
  </requirements>


<stdio>
    <exit_code range="1:" level="fatal" />
</stdio>


<command> <![CDATA[
   if [ -d $__root_dir__/packages/scilab-6.1.0 ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else scilab-cli -nb -quit -f $* < ${script_file}; fi
]]>
</command>


  <configfiles>
    <configfile name="script_file">
        <![CDATA[ exec("$__tool_directory__/src/mz_hdf5tosci.sci",-1); ...
        if ~isdef('pls') then ...
           atomsSystemUpdate(); ...
           atomsInstall('FACT'); ...
           atomsLoad('FACT'); ...
        end; ...
        lasterror(); ...
        res=mz_hdf5tosci("${filein}"); ...
        save("${res}",'res'); ...
        if ~isempty(lasterror(%f)) then ...
        write(0,lasterror()); ...
        end ]]>
    </configfile>
  </configfiles>


  <inputs>
     <param name="filein"       format="h5"                type="data"      label="Mass spectrum, .h5 format"    />
  </inputs>
  

  <outputs>
      
      <data name="res"      format="mat"             label="${filein.name}.dat"  />
    
  </outputs>
 
 
  <tests>
    <test>
       <param name="filein" value="VI2016_AC_4Areduit_1.h5"/>
       <output name="res"   file="VI2016_AC_4Areduit_1.dat" compare="sim_size" delta="500" />
    </test>
  </tests>

 <help>


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


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

=================
MS .h5 -> MS .dat
=================

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

This function converts an Orbitrap HDF5 mass spectrum into a Scilab mass spectrum

-----
Input
-----

**an .h5 hrms**

Previously, Orbitrap devices yielded .raw files.

MSconvert selected MS1 and performed the conversion .raw -> .md5 

Then HDF5View performed the conversion .md5 -> .h5 
which is the format of the input file.


-------
Outputs
-------

**a .dat mass spectrum**

This is an HDF5 file whose structure is specific to Scilab.

It contains two fields:

- time: the retention times, a vector;

- mzdata: a list containing a MS1 spectrum (m/z + signals) for each retention time.


</help>

<citations> 

</citations>



</tool>