changeset 12:3a9c0c99bb54 draft

avec scilab-6.1.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/detrend_sci.xml	Fri Jun 25 09:24:37 2021 +0000
@@ -0,0 +1,126 @@
+<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>