# HG changeset patch
# User jcb-mpl
# Date 1652357563 0
# Node ID 6e260ccff3d8dfdf708e87a7c643fdc1b98cb0a6
# Parent  64c2025cd389f48507f4d101de3225b3d27811c6
Uploaded

diff -r 64c2025cd389 -r 6e260ccff3d8 eics_compression.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eics_compression.xml	Thu May 12 12:12:43 2022 +0000
@@ -0,0 +1,134 @@
+<tool id="2021_05_eics_compression" name="MS-centroid -> compression" version="0.0.1">
+    <description> by a factor k  </description>
+
+
+  <requirements>
+    <requirement type="package" version="6.0.2">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_1_out_of_k.sci",-1); ...
+        exec("$__tool_directory__/src/mz_1_merge_by_k.sci",-1); ...
+        lasterror(); ...
+        k=${k}; ...
+        option=${option}; ...
+        load("${resbary_in}"); ... // the variable name must be resbary
+        if option==1 then ...
+            resbary_out=mz_1_out_of_k(resbary,k); ...
+        else ...
+            resbary_out=mz_1_merge_by_k(resbary,k); ...
+        end; ...
+        if ~isdef('resbary_out') then ...
+           disp('resbary_out is not defined'); ...
+        end; ...
+        resbary=resbary_out; ...  // the variable name must be resbary
+        save("${resbary_out}",'resbary'); ...
+        if ~isempty(lasterror(%f)) then ...
+        write(0,lasterror()); ...
+        end; ]]>
+    </configfile>
+  </configfiles>
+
+
+  <inputs>
+    <param name="resbary_in"       format="mat"         type="data"      label="MS-centroid"  help="contains the fields .time et .mzdata"   />
+    <param name="k"     value="1"  type="integer"     min="1"   max="100"   label="k"        help="a number of RTs"     />
+  <param name="option"     value="2"  type="integer"     min="1"   max="2"   label="option"        help="1= 1 out of k RT; 2= mean of k RT"     />
+</inputs>
+
+  <outputs>
+    <data name="resbary_out"   format="mat"     label="MS-compressed"  />
+  </outputs>
+  
+  
+  <tests>
+  
+    <test>
+       <param name="resbary_in" value="VI2016_AC_4Areduit_1centroide.mat"/>
+       <param name="k" value="3"/>
+       <param name="option" value="1"/>
+       <output name="resbary_out"   file="VI2016_AC_4Acentroide-1_k1outof3.mat" compare="sim_size" delta="1000" />
+    </test>
+    
+    <test>
+       <param name="resbary_in" value="VI2016_AC_4Areduit_1centroide.mat"/>
+       <param name="k" value="3"/>
+       <param name="option" value="2"/>
+       <output name="resbary_out"   file="VI2016_AC_4Acentroide-1_k_3mean.mat" compare="sim_size" delta="1000" />
+    </test>
+    
+    
+    
+  </tests>
+  
+  
+  
+<help>
+
+
+**Authors**  Jean-Claude Boulet (INRAE).
+
+
+---------------------------------------------------
+
+=================================
+COMPRESSION OF A CENTROID MS DATA
+=================================
+
+
+-----------
+Description
+-----------
+
+This function reduces by a factor k the number of RTs and associated mass spectra. 
+
+
+-----
+Input
+-----
+
+**centroid MS data**
+
+A centroid MS data, at the HDF5-scilab format.
+
+**k**
+
+The compression factor. 
+
+**option**
+
+- 1: selects one out of k RTs and associated ms.
+
+- 2: merges by k the RTs and associated ms 
+
+
+-------
+Outputs
+-------
+
+**compressed MS data**
+
+A centroid MS data, similar to the input, but with k times less RTs and ms. 
+
+</help>
+
+
+<citations>
+
+</citations>
+
+
+</tool>