view detrend_sci.xml @ 13:0cd4026ab644 draft default tip

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<tool id="V20.10_detrend_sci" name="DT" version="20.05">
  <description>Detrend</description>
 
<requirements>
   <requirement type="package" version="6.0.2" >scilab</requirement> 
</requirements>

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

<command><![CDATA[ 
if [ ! -d /data/singularity ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else /usr/local/bin/singularity exec -B /data /data/singularity/scilab.sif scilab-cli -nb -quit -f $* < ${script_file}; fi
]]>
 </command>

 <configfiles>
    <configfile name="script_file">
      lasterror(); ...
      if ~isdef('pls') then ...
      atomsInstall('FACT'); ...
      atomsLoad('FACT'); ...
      end; ...
      lasterror(%f); ...
      x=glx_tab2div("${Xdata.file_name}"); ...
      x2=detrending(x,${degre}); ...
      div2tab(x2,"${DT}"); ...
      if ~isempty(lasterror(%f)) ...
      write(0,lasterror()) ...
      end
    </configfile>
  </configfiles>

 <inputs>
    <param name="Xdata" type="data" format="tabular"  label="Select X data" help="Dataset (n x p) containing the n spectra of p variables."/>
    <param name="degre" type="integer" value="2" min="0" max="5" label="Degree of the polynom"/>
  </inputs>

  <outputs>
    <data name="DT" format="tabular" label="DT(${Xdata.name})" />
  </outputs>
 
  <tests>
    <test>
      <param name="Xdata" value="test_detrend_input.tabular"/>
      <param name="degre" value="2" />
    
      <output name="DT" >
      <assert_contents> 
          <has_text text="0.000838"/>
          <has_text text="-0.000194"/>
          <has_text text="-0.000131"/>
          <has_text text="0.001114"/>
      </assert_contents>
       </output>

    </test>
  </tests> 

<help>

.. class:: warningmark

**TIP:** If your data is not TAB delimited, use *Convert format data Tools-&gt;Convert*

.. class:: infomark

**Authors** Fabien Gogé (IRSTEA), Virginie Rossard (INRA), Eric Latrille (INRA), Jean-Michel Roger (IRSTEA), Jean-Claude Boulet (INRA)


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

=======
DETREND
=======

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


Performs **Detrend**, a  baseline correction by orthogonal projection onto a n-order polynomial.
Missing values are not allowed. This scripts uses the FACT-version module.


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

A matrix of numeric data with headers (tabular format) and decimal separator ".".


+--------+-------+--------+
| Name   | 400   | 402    |
+========+=======+========+
|M102T645| 0.63  |0.64    |
+--------+-------+--------+
|M105T604| 0.5   |0.49    |
+--------+-------+--------+

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

**Degree of the polynom**

The degree of the polynom used in the Detrend correction

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

**DT(input.file_name)**

A dataset containing the input file after the Detrend correction; format = tabular.

</help>

<citations>

  <citation type="doi">10.1366/0003702894202201</citation> 

 </citations>


</tool>