# HG changeset patch
# User jcb-mpl
# Date 1652357601 0
# Node ID 50d9f45f2182f1b1d9e9baaf97b28a8ee6960e3c
# Parent  4e9b2d0c010bb6948a287d2879836ff6ee212e78
Deleted selected files

diff -r 4e9b2d0c010b -r 50d9f45f2182 2018_07_first_eics.xml
--- a/2018_07_first_eics.xml	Thu May 12 12:13:15 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,169 +0,0 @@
-<tool id="2021_05_mz_eics_individual" 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[ 
-  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_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>
-
-
-
-
-