changeset 3:b82aec727e31 draft default tip

Deleted selected files

--- a/2018_07_check_reference_mz.xml	Thu May 12 12:11:34 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,154 +0,0 @@
-<tool id="2021_05_check_ref_mz" name="EICs -> checks reference mz" version="0.0.1">
-  
-  <description> for 5 determined thresholds for m/z  </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_0_publi_features4_galaxy.sci",-1); ...
-        exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
-        lasterror(); ...
-        ...
-        x_in=glx_tab2div("${xtrmz4}"); ...  // 20avril21
-        [x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}",x_in, ${electron}); ...
-        ... //[x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}", "${xtrmz4}", ${electron}); ...
-        ...
-        div2tab(x_bilan, "${xbilan}"); ...
-        save("${xsynthese}","x_synthese"); ...
-        save("${x_tr_mz_trouves}","x_tr_mz4"); ...
-        if ~isempty(lasterror(%f)); ...
-        write(0,lasterror()); ...
-        end; ]]>
-    </configfile>
-  </configfiles>
-
- 
-  <inputs>
-    <param name="mzref"       format="tabular"            type="data"      label="Reference m/z values"    />
-    <param name="xtrmz4"      format="tabular"            type="data"      label="EICs-mean"    />
-    <param name="electron"    size="5"       value="0"    type="integer"   label="Electron mass" help="1=correction of the reference m/z values; 0=no correction"    />
-  </inputs>
-
-
-  <outputs>
-    <data name="xbilan"           format="tabular"      label="m/z check-summary"  />
-    <data name="xsynthese"        format="mat"          label="m/z check-details"  />
-    <data name="x_tr_mz_trouves"  format="mat"          label="m/z check-matrix"   />
-  </outputs>
-  
-  
-  <tests>
-  
-    <test>
-       <param  name="mzref"                 value="ref_mz.tab"/>
-       <param  name="xtrmz4"                value="EICs-merged.tab"/>
-       <output name="xbilan">
-           <assert_contents> 
-       	<has_text text="0.00034"/>
-       	<has_text text="0.352"/>   
-           </assert_contents>
-       </output>
-    </test>
-    
-  </tests>
-<help>
-
-
-**Author**  Jean-Claude Boulet (INRA).
-
-
----------------------------------------------------
-
-=======================================================================
-CHECK REFERENCE MZ VALUES AMONG THE EICS-MEAN YIELDED BY THE PROCESSING
-=======================================================================
-
------------
-Description
------------
-
-A matrix of EICs has been yielded by the function: MS-centroid -> EICs-individual or by the function: several EICs-shared -> one EICs-mean.
-
-The m/z values of these EICs are compared to reference m/z values for 5 pre-determined threshold values for m/z: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100. 
-
-This function is focused on the m/z values, it does not take into account the retention times. 
-
-
-
-------
-Inputs
-------
-
-**reference m/z values**
-
-A tabular file, to the div format (first columns and rows = labels):
-
-- the first column corresponds to names of chemical compounds;
-
-- the second column contains the exact (reference) m/z values.
-
-
-**EICs-mean or individual**
-
-A tabular matrix of (RT x m/z); lines are retention times and columns are EICs.
-
-
-----------
-Parameters
-----------
-
-**correction of the electron mass**
-
-A correction can be applied to the reference m/z values. 
-
-- 0: no correction;
-
-- 1: correction = subtraction of 0.00055 in the positive mode. 
-
-
-
-------
-Output
-------
-
-**summary**
-
-The main results  
-
-
-**details**
-
-A .mat file
-
-
-**extracted EICs**
-
-An EIC is associated to a reference m/z value if the absolute difference of (EIC minus reference) is under a threshold. 
-
-Five threshold values have been pre-determined: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100
-
-This output contains a list of 5 data, each containing the EICs identified as reference m/z values according to a threshold. 
-
-</help>
-
-
-<citations>
-
-</citations>
-
-
-</tool>