# HG changeset patch
# User jcb-mpl
# Date 1652357595 0
# Node ID 4e9b2d0c010bb6948a287d2879836ff6ee212e78
# Parent  2e517ac29e6cb2dde6f7d2bd75a9504daba59b88
Uploaded

diff -r 2e517ac29e6c -r 4e9b2d0c010b eics_first_extraction.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eics_first_extraction.xml	Thu May 12 12:13:15 2022 +0000
@@ -0,0 +1,169 @@
+<tool id="2021_05_mz_eics_first_extraction" name="MS-centroid -> EICs-individual"  version="0.0.2">
+
+  <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_3_extract_all_mz2.sci",-1); ...
+        exec("$__tool_directory__/src/mz_4_scan_mz_raw6.sci",-1); ...
+        exec("$__tool_directory__/src/mz_5_tr_matrix6bis.sci",-1); ...
+        exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
+        exec("$__tool_directory__/src/mz_6_rescan_mz2.sci",-1); ...
+        exec("$__tool_directory__/src/mz_7_dwcleaning.sci",-1); ...
+        exec("$__tool_directory__/src/mz_eic5_step2.sci",-1); ...
+        lasterror(); ...
+        load("${resbary}"); ...
+        if ~isdef('resbary'); ...
+           error('resbary is not defined'); ...
+        end; ...
+        diffmz=${diffmz}; ...
+        set=${signaleicthresh}; ...
+        dw=${dw}; ...
+        x_tr_mz3=mz_eic5_step2(resbary,diffmz,set,dw); ...
+        ... //save("${x_tr_mz3}",'x_tr_mz3'); ...
+        div2tab(x_tr_mz3,"${x_tr_mz3}"); ...  // 22avril21
+        if ~isempty(lasterror(%f)); ...
+            write(0,lasterror()); ... 
+        end; ]]>
+  </configfile>
+  </configfiles>
+
+
+  <inputs>
+    <param name="resbary"         format="mat"       type="data"      label="MS-centroid"    />
+    <param name="diffmz"          value="0.0024"     type="float"     label="Threshold for the m/z values" />
+    <param name="signaleicthresh" value="30000"      type="integer"   label="Threshold for the signals"  />
+    <param name="dw"              value="1"          type="float"     label="Threshold for Durbin-Watson"  help="to remove noisy EICs" />
+  </inputs>
+  
+  
+  <outputs>
+    <data name="x_tr_mz3"   format="tabular"     label="EICs-individual"  />
+  </outputs>
+  
+  
+  <tests>
+    
+      <test>
+       <param name="resbary" value="VI2016_AC_4Acentroide-1_k_3mean.mat"/>
+       <param name="diffmz" value="0.0024"/>
+       <param name="signaleicthresh" value="30000"/>
+       <param name="dw" value="1"/>
+       <output name="x_tr_mz3"   file="EICs-individual-1_k3mean.tab" compare="sim_size" delta="1000" />
+    </test>
+    
+  </tests>
+
+
+<help>
+
+
+**Author**  Jean-Claude Boulet (INRAE).
+
+
+---------------------------------------------------
+
+==========================================
+EXTRACTION OF EICS FROM A CENTROID MS DATA
+==========================================
+
+-----------
+Description
+-----------
+
+The HRMS analysis of a samples yields a MS data.  
+
+From a centroid MS data, a matrix of (RT x m/z) is extracted.
+
+Each column of this matrix is an EIC = Extracted Ion Chromatogram, i.e. the signals of a given m/z value along the retention times. 
+
+------
+Inputs
+------
+
+**MS-centroid**
+
+It is an HDF5-Scilab structure obtained by the previous processings and containing the fields: 
+
+- resbary.time: the retention times;
+
+- resbary.mzdata: the mass spectra associated to the RTs.
+
+
+
+----------
+Parameters
+----------
+
+Three thresholds have to be determined. 
+
+
+**Threshold for the m/z values** 
+
+The difference between two m/z values is compared to the threshold; if lower, the m/z values are considered as the same and merged; if higher the m/z values are considered as different. 
+
+Default value: 0.0024. 
+
+
+**Threshold for the signals**
+
+The EICs whose global signal is under this threshold are dropped from the EIC matrix. 
+
+Default value: 30000.
+
+
+**Threshold for Durbin-Watson**
+
+Durbin-Watson values can range between 0 and 2. 
+
+EICs with a DW value higher than the threshold are considered as noise and therefore dropped. 
+
+Default value: 1.
+
+
+
+-----
+Oupts
+-----
+
+**EIC-individual matrix**
+
+A matrix of signal intensities obtained from a single MS: 
+
+- rows are the retention times;
+
+- columns are the m/z values determined by the processing.
+
+The file is a .dat HDF5-Scilab format.  
+
+</help>
+
+
+<citations>
+
+</citations>
+
+
+</tool>
+
+
+
+
+