changeset 5:e2541ea9c53c draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eics_merged.xml	Thu May 12 12:54:52 2022 +0000
@@ -0,0 +1,103 @@
+<tool id="2021_05_eics_merged" name="EICs-synchronized -> EICs-merged" version="0.0.1">
+
+  <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_8_merge_list_x_tr_mz4.sci",-1); ...
+      lasterror(); ...
+      load("${list_eic4_files}");  ...  // the variable name is also: list_eic4_files
+      [x_tr_mz4,ppm_coupe]=mz_8_merge_list_x_tr_mz4(list_eic4_files); ...
+      div2tab(x_tr_mz4,"${merged_x_tr_mz4file}"); ...
+      if ~isempty(lasterror(%f)) then ...
+        write(0,lasterror()); ...
+      end; ]]>
+    </configfile>
+  </configfiles>
+
+
+  <inputs>
+    <param name="list_eic4_files"  format="mat"  type="data" label="Select X data" help="a list of EIC-synchronized files with all the same mz values "/>
+  </inputs>
+
+
+  <outputs>
+    <data name="merged_x_tr_mz4file" format="tabular"  label="EICs-merged"/>
+  </outputs>
+  
+  
+  <tests>
+  
+    <test>
+       <param  name="list_eic4_files"       value="EICs-synchronized.mat"/>
+       <output name="merged_x_tr_mz4file"   file="EICs-merged.tab" compare="sim_size" delta="1000" />
+    </test>
+    
+  </tests>
+  
+<help>
+
+
+.. class:: infomark
+
+**Authors** Jean-Claude Boulet (INRAE)
+
+
+---------------------------------------------------
+
+==========================
+MEAN OF SEVERAL EICS FILES
+==========================
+
+-----------
+Description
+-----------
+
+Several EIC files correspond to the same sample (e.g. repetitions). They share the same m/z values, not necessary the same retention times even if their RTi should be close.
+
+This function merges them into a single (RT x m/z) dataset
+
+
+-----------
+Input files
+-----------
+
+**Select Xdata**
+
+At least two datasets, gathered into a single HDF5-scilab .dat file issued from the function: EICs-individual - EICs-synchronized
+
+------------
+Output files
+------------
+
+**EICs-merged**
+
+The merged EICs in a tabular file.
+
+
+</help>
+
+
+<citations>
+
+</citations>
+
+</tool>