changeset 1:c1008b92a6c8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/features_check_references.xml	Thu May 12 12:15:10 2022 +0000
@@ -0,0 +1,175 @@
+<tool id="2021_05_features_check_references" 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[ 
+      $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file} 
+      ]]>
+  </command>
+  
+
+  <configfiles>
+    <configfile name="script_file">
+        <![CDATA[ exec("$__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>
+
+