# HG changeset patch
# User jcb-mpl
# Date 1652357757 0
# Node ID 7e757edfa3b067a0bdbead51cc4fb7986988de14
# Parent  247771a356a72fb9d1a6501b7c74600a3f796342
Deleted selected files

diff -r 247771a356a7 -r 7e757edfa3b0 2018_07_extract_peaks.xml
--- a/2018_07_extract_peaks.xml	Thu May 12 12:15:52 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,203 +0,0 @@
-<tool id="2021_05_extract_features" name="EICs -> Peaks:features" version="0.0.1">
-      <description> extracts the peaks (m/z x TR) from the EICs </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_8_peakpicking_dw.sci",-1); ...
-        exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
-        lasterror(); ...
-        option=${option}; ...
-        if option==1 then ...      // liste ou fichier .dat
-            load("${list_eic4_files}"); ...
-            list_var=who_user(%f); ...
-            n=size(list_var,1); ...
-            for i=1:n; 
-               execstr(msprintf("type_tmp=type(%s);",list_var(i))); ...
-               if type_tmp==15 then ...
-                   execstr(msprintf("x_tr_mz4=%s;",list_var(i))); ...
-                   break;...
-               end; ...
-            end; ...   
-        ...      
-        elseif option==2 then ...  // tabular 
-            x_tr_mz4=glx_tab2div("${list_eic4_files}"); ...
-        end; ...
-        ...
-        if isdef('x_tr_mz3'); ...
-            x_tr_mz4=x_tr_mz3; ...
-        end; ...
-        ...
-        if typeof(x_tr_mz4)=="list"; ...
-            x_tr_mz4_i=x_tr_mz4(${no}); ...
-        elseif typeof(x_tr_mz4)=="div"; ...
-            x_tr_mz4_i=x_tr_mz4; ...
-        end; ...
-        ...
-        [peaks_list,peaks_detail]=mz_8_peakpicking_dw(x_tr_mz4_i,[1:$],${plage_tr},${plage_min_tr},${dw_max},${signal_min},0); ...
-        ...
-        peaks_list.i='eic n0 '+ peaks_list.i; ...
-        div2tab(peaks_list,"${peaks_list}"); ...  // 20avril21
-        ... // save("${peaks_list}",'peaks_list'); ...
-        save("${peaks_detail}",'peaks_detail'); ...
-        ...
-        if ~isempty(lasterror(%f)); ...
-            write(0,lasterror()); ...
-        end; ]]>
-        </configfile>
-     </configfiles>
-
-
-    <inputs>
-    <param name="list_eic4_files"     format="mat,tabular"            type="data"      label="EICs files"          help="a list of several files, or a single matrix EIC matrix  (RT x m/z)" />
-    <param name="option"     value="2"  type="integer"     min="1"   max="2"   label="Type of data"        help="1= a list from the function: EIVs -> check reference mz; 2= an EIC matrix, e.g. from the function: EICs-synchronized -> EICs-merged"     />
-    <param name="no"             size="5"     value="1"       type="integer"   label="Number"                         help="if list, from 1 to 5 " />
-    <param name="plage_tr"       size="5"     value="0.3"     type="float"     label="Maximum range of RT "           help="in minutes" />
-    <param name="plage_min_tr"   size="5"     value="0.05"    type="float"     label="Minimum range of RT "           help="in minutes"           />
-    <param name="dw_max"         size="5"     value="1"       type="float"     label="Threshold for Durbin-Watson"    help="a value between 0 and 2"   />
-    <param name="signal_min"     size="5"     value="100000"   type="float"     label="Threshold for the signal max"   help="peaks with signal max under this value are dropped"   />
-    
-  </inputs>
-
-
-  <outputs>
-    <data name="peaks_list"     format="tabular"    label="Peaks list"/>
-    <data name="peaks_detail"   format="mat"        label="Peaks details"    />
-  </outputs>
-
-
-  <tests>
-  
-    <test>
-       <param  name="list_eic4_files"     value="x4_list.dat"/>
-       <param  name="option"              value="1"/>
-       <param  name="no"                  value="3"/>
-       <param  name="plage_tr"            value="0.3"/>
-       <param  name="plage_min_tr"        value="0.05"/>
-       <param  name="dw_max"              value="1"/>
-       <param  name="signal_min"          value="100000"/>
-       <output name="peaks_list">
-           <assert_contents> 
-       	<has_text text="0.2020"/>
-       	<has_text text="0.8740"/>
-       	<has_text text="3.2942"/>  
-           </assert_contents>
-       </output>
-    </test>
-    
-    <test>
-       <param  name="list_eic4_files"     value="x4.tab"/>
-       <param  name="option"              value="2"/>
-       <param  name="plage_tr"            value="0.3"/>
-       <param  name="plage_min_tr"        value="0.05"/>
-       <param  name="dw_max"              value="1"/>
-       <param  name="signal_min"          value="100000"/>
-       <output name="peaks_list">
-           <assert_contents> 
-       	<has_text text="0.2020"/>
-       	<has_text text="0.8740"/>
-       	<has_text text="3.2942"/>  
-           </assert_contents>
-       </output>
-    </test>
-      
-  </tests>
-  
-  
-  <help>
-
-
-**Authors**  Jean-Claude Boulet (INRA).
-
-
----------------------------------------------------
-
-=========================
-PEAKS:FEATURES EXTRACTION
-=========================
-
------------
-Description
------------
-
-A feature or peak is a signal recorded for a given m/z value and a range of retention times. 
-
-This function extracts the peaks of each EIC from an EIC matrix. 
-
-Note: this features extraction algorithm does not claim novelty nor higher performances. But it corresponds well to our outputs. For a basic use. 
-
-
-
------
-Input
------
-
-**EICs files**
-
-- a matrix from e.g. the function: EICs-synchronized -> EICs-merged 
-
-- or a list yielded by the function: EICs -> checks reference mz
-
-
-----------
-Parameters
-----------
-
-**Number**
-
-In case of a list, the number to select, from 1 to 5, corresponding to the m/z thresholds of 0.0005, 0.0010, 0.0030, 0.0050 and 0.0100 respectively 
-
-**Maximum range of retention time**
-
-Default value: 0.3 
-
-
-**Minimum range of retention time**
-
-Default value: 0.05
-
-**Threshold for Durbin-Watson**
-
-Default value: 1 
-
-
--------
-Outputs
--------
-
-**Peaks list**
-
-A file of 4 columns: RT min, RT max, m/z value and signal
-
-**Peaks detail**
-
-The file, format HDF5-scilab, contains a list. 
-
-Each element of the list is associated to a peak, i.e. a line of the Peaks List output. 
-
-Each element of the list contains a column vector of the signals recorded along a range of retention times, identified by the line labels. The column label is the m/z value of the peak. 
-
-</help>
-
-
-<citations>
-
-</citations>
-
-
-</tool>