changeset 2:05a5f68935f2 draft default tip

Deleted selected files

--- a/2018_07_mz_synchronized.xml	Thu May 12 12:14:37 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-<tool id="2021_05_eics_synchronized" 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[ 
-    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_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-shared"/>
-  </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>