# HG changeset patch
# User jcb-mpl
# Date 1652357716 0
# Node ID edc94aa0b5c40a2ff4f2fce7ac66ec7d0ea9de92
# Parent  c1008b92a6c81a1778ab7b0426253a75949a5d41
Deleted selected files

diff -r c1008b92a6c8 -r edc94aa0b5c4 2018_07_check_peaks.xml
--- a/2018_07_check_peaks.xml	Thu May 12 12:15:10 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,175 +0,0 @@
-<tool id="2021_05_checks_ref_features" name="Features -> checks references" version="0.0.1">
-
-  <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_9_compares_peaks.sci",-1); ...
-        lasterror(); ...
-        ... //load "${peaks_list}"; ... // 22avril21
-        peaks_list=glx_tab2div("${peaks_list}"); ...
-        ...
-        load "${peaks_detail}"; ...
-        x836=glx_tab2div("${peaks_reference}"); ...
-        diff_mz=${diff_mz}; ...
-        k=${k}; ...
-        x_peaks_final=mz_9_compares_peaks(peaks_list,peaks_detail,x836,diff_mz,k); ...
-        ...
-        div2tab(x_peaks_final,"${x_peaks_final}"); ... 
-        if ~isempty(lasterror(%f)); ...
-            write(0,lasterror()); ...
-        end; ]]>
-    </configfile>
-  </configfiles>
-
-
-  <inputs>
-    <param name="peaks_list"      format="tabular"     type="data"      label="Features list"   help="from function  EIC->peaks:features"    />
-    <param name="peaks_detail"    format="mat"     type="data"      label="Detailed features"     help="from function  EIC->peaks:features"  />
-    <param name="peaks_reference" format="tabular" type="data"      label="Reference features"     help="2columns: mz and RT, with column and line headers" />
-    <param name="diff_mz"         value="0.0050"   type="float"     label="Threshold for m/z values" />
-    <param name="k"               value="1"        type="integer"   label="Number of extracted features for each reference feature"  help="the closest to the reference peak" />
-   
-  </inputs>
-  
-  
-  <outputs>
-    <data name="x_peaks_final"   format="tabular"  label="Identified features" />
-  </outputs>
-  
-  
-  <tests>
-  
-  <test>
-       <param  name="peaks_list"          value="Peaks_list.tabular"/>
-       <param  name="peaks_detail"        value="Peaks_details.mat"/>
-       <param  name="peaks_reference"     value="ref_mz_rt.tab"/>
-       <param  name="diff_mz"             value="0.0050"/>
-       <param  name="k"                   value="1"/>
-       <output name="x_peaks_final">
-           <assert_contents> 
-       	<has_text text="136.0616"/>
-       	<has_text text="229.135"/>   
-           </assert_contents>
-       </output>
-    </test>
-    
-  </tests>
-
-
-<help>
-
-
-**Author**  Jean-Claude Boulet (INRA).
-
-
----------------------------------------------------
-
-==================================
-FEATURES EXPERIMENTAL VS REFERENCE
-==================================
-
-
------------
-Description
------------
-
-This function checks reference features among experimental features. 
-
------------
-Input files
------------
-
-**Features list**
-
-The tabular file yielded by the function: EICs -> peaks:features
-
-
-**Detailed features**
-
-The HDF5-scilab file yielded by the function: EICs -> peaks:features
-
-
-**Reference features**
-
-A tabular file containing 2 columns: m/z values then retention times
-
-Row labels are the names of the reference features, e.g. chemical compounds
-
-
-
-----------
-Parameters
-----------
-
-**Threshold for m/z values**
-
-Observed features are associated to the reference features if 1) the difference in m/z values is under the threshold; 2) the reference RT falls within the range of the observed RTs.
-
-Default: 0.0050
-
-**Number of extracted features for each reference feature**
-
-e.g. if the number is 2, the algorithm will extract the 2 experimental features closest to each reference feature.
-
-
-------
-Output
-------
-
-
-**Identified features**
-
-A tabular file with the columns: 
-
-- name of the reference feature
-
-- number of the reference feature in the input file: Reference features
-
-- number of the experimental feature in the input files: Features List and Detailed features
-
-- number of identifications= the number of reference features each experimental feature has been attributed to; target = 1 
-
-- m/z value of the reference feature
-
-- m/z value of the experimental feature 
-
-- difference of m/z values
-
-- RT of the reference feature
-
-- RT of the experimental feature 
-
-- difference of RT 
-
-- signal of the experimental feature 
-
-
-</help>
-
-
-<citations>
-
-</citations>
-
-
-</tool>
-
-