changeset 1:807674410cf6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eics_synchronization.xml	Thu May 12 12:14:37 2022 +0000
@@ -0,0 +1,139 @@
+<tool id="2021_05_eics_synchronization" name="EICs-individual -> EICs-synchronized" version="0.0.1">
+
+  <description>  for a series of close mass spectra, e.g. repetitions  </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_4_extract_final_mz_v3.sci",-1); ...
+      lasterror(); ...
+      col=list(); ...
+      #for $i, $s in enumerate( $series )
+        x_tr_mz3=glx_tab2div("${s.Xdata.file_name}"); ...
+        ... //  load("${s.Xdata.file_name}"); ...  22avril21
+        x${i}=x_tr_mz3; ...
+        col(${i}+1)=x${i}; ...
+      #end for
+      ...
+      [list_eic4_files,mz4_stats]=mz_4_extract_final_mz_v3(col,${delta_mz}); ...
+      save("${list_eic4_files}",'list_eic4_files'); ...
+      save("${mz4_stats}",'mz4_stats'); ...
+      if ~isempty(lasterror(%f)) then ...
+        write(0,lasterror()); ...
+      end; ]]> 
+    </configfile>
+  </configfiles>
+
+
+  <inputs>
+    <repeat    name="series"    title="dataset" min="2">
+        <param name="Xdata"     format="tabular"    type="data"  label="Input file"  help="EICs-individual files"/>
+    </repeat>
+    <param     name="delta_mz"  value="0.0024"  type="float" label="Threshold for m/z"  />
+  </inputs>
+
+
+  <outputs>
+    <data name="list_eic4_files" format="mat"   label="EICs-synchronized"/>
+    <data name="mz4_stats"       format="mat"   label="stats on EIC-synchro"/>
+  </outputs>
+
+
+  <tests>
+
+     <test>
+       <param name="Xdata" value="EICs-individual-1_k3mean.tab"/>
+       <param name="Xdata" value="EICs-individual-2_k3mean.tab"/>
+       <param name="Xdata" value="EICs-individual-3_k3mean.tab"/>
+       <param name="delta_mz"     value="0.0024"/>
+       <output name="list_eic4_files"   file="EICs-synchronized.mat" compare="sim_size" delta="1000" />
+    </test>
+    
+  </tests>
+
+
+<help>
+
+
+.. class:: infomark
+
+**Author** Jean-Claude Boulet (INRAE)
+
+
+---------------------------------------------------
+
+=================================================
+EXTRACTS THE EICS SHARED BY A SERIES OF EIC FILES
+=================================================
+
+-----------
+Description
+-----------
+
+The EICs shared by a series of EICs-individual are identified. 
+
+Then, each of the initial EiCs-individual is reprocessed as to keep only the EICs shared by all the series.  
+
+The main application is the synchronization of the EICs of repetitions.
+
+
+
+-----------
+Input files
+-----------
+
+At least two EICs-individual
+
+----------
+Parameters
+----------
+
+**Threshold for m/z**
+
+Two m/z values whose difference is larger than this threshold will be considered as different. 
+
+Default value: 0.0024
+
+
+------------
+Output files
+------------
+
+
+**EICs-shared**
+
+The input files with the same EICs. 
+
+A list at the HDF5-scilab .dat format. 
+
+
+
+**stats on EICs-shared**
+
+Some calculations for the following processings. 
+
+</help>
+
+
+<citations>
+
+</citations>
+
+</tool>