# HG changeset patch
# User genouest
# Date 1635515949 0
# Node ID 9072a2d2178b927b87b3eb7a0dd2021bcf8f8867

"planemo upload commit c24cf4eadc45f2915f24cae2940c81c12dd3aab4"

diff -r 000000000000 -r 9072a2d2178b P2M2WorkflowsTools-assembly-0.1.4.jar
Binary file P2M2WorkflowsTools-assembly-0.1.4.jar has changed
diff -r 000000000000 -r 9072a2d2178b README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Oct 29 13:59:09 2021 +0000
@@ -0,0 +1,16 @@
+### generation avec planemo
+
+```
+cp ../../target/scala-2.13/P2M2WorkflowsTools-assembly-*.jar .
+```
+
+dans openlabcds2csv.xml balise <command>
+
+`openlabcds2csv` doit etre remplacer par `java -jar '$__tool_directory__/P2M2WorkflowsTools-assembly-xxxx.jar'`
+
+planemo l
+planemo t
+
+### todo
+
+paquet bioconda
diff -r 000000000000 -r 9072a2d2178b openlabcds2csv.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/openlabcds2csv.xml	Fri Oct 29 13:59:09 2021 +0000
@@ -0,0 +1,40 @@
+<tool id="openlabcds2csv" name="Converting multiple OpenLabCDS Text Files to a CSV summary file" version="0.1.0" profile="21.05">
+    <requirements>
+        <requirement type="package" version="8.0.121">openjdk</requirement> 
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      java -cp '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.4.jar' fr.inrae.metabolomics.p2m2.OpenLabCDS2CsvCommand
+       #for $input in $input_openlabscds_files
+         #if $input
+           $input
+         #end if
+        #end for
+        --out '$output_csv' --column '$column'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_openlabscds_files" multiple="true" format="txt" />
+        <param type="select" name="column" label="target column to build as summary">
+		<option value="RetTime">RetTime</option>
+		<option value="Type">Type</option>
+		<option value="ISTD">ISTD</option>
+		<option value="Area" selected="true">Area</option>
+		<option value="Amt/Area">Amt/Area</option>
+		<option value="Amount">Amount</option>
+                <option value="Grp">Grp</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_csv" format="csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_openlabscds_files" value="Report_Ex1.txt,Report_Ex2.txt,Report_Ex3.txt"/>
+            <param name="column" value="Area"/>
+            <output name="output_csv" file="Results.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+       Get multiple "Internal Standard Report" from the OpenLabCDS software where are describe a list of compound in format row (columns : RetTime  Type  ISTD    Area     Amt/Area    Amount   Grp   Name)
+       The converter creates a summary that contains a header (a list of compounds) and a list of "Sample name" with associated values ​​for a target column (RetTime,Type,ISTD,Area,Amt/Area,Amount,Grp,Name)
+    ]]></help>
+</tool>
diff -r 000000000000 -r 9072a2d2178b test-data/Report_Ex1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Report_Ex1.txt	Fri Oct 29 13:59:09 2021 +0000
@@ -0,0 +1,53 @@
+Data File C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\Std 500.D
+Sample Name: EX1
+MPSr-GCFID 10/19/2021 2:39:33 PM SYSTEM
+
+=====================================================================
+Acq. Operator   : SYSTEM                         Seq. Line :   8
+Sample Operator : SYSTEM                                                                     
+Acq. Instrument : MPSr-GCFID                      Location :   6  (F)
+Injection Date  : 10/11/2021 11:03:47 PM               Inj :   1
+                                                Inj Volume : 1 µl
+Acq. Method     : C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\190314_
+                  Glucides_prep_12-110.M
+Last changed    : 2/25/2021 3:02:59 PM by SYSTEM
+Analysis Method : C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\190314_
+                  Glucides_retraitement.M
+Last changed    : 10/19/2021 2:39:30 PM by SYSTEM
+                  (modified after loading)
+Additional Info : Peak(s) manually integrated
+=====================================================================
+                      Internal Standard Report                       
+=====================================================================
+
+Sorted By             :      Signal
+Calib. Data Modified  :      10/15/2021 5:02:32 PM
+Multiplier            :      1.0000
+Dilution              :      1.0000
+Sample Amount:        :    100.00000  [ng/ul]   (not used in calc.)
+Use Multiplier & Dilution Factor with ISTDs
+Sample ISTD Information:
+ISTD  ISTD Amount   Name
+  #    [ng/ul]  
+----|-------------|-------------------------
+  1    100.00000   Adonitol
+
+
+Signal 1: FID1 A, 
+
+RetTime  Type  ISTD    Area     Amt/Area    Amount   Grp   Name
+ [min]         used  [pA*s]      ratio     [ng/ul]  
+-------|------|----|----------|----------|----------|--|------------------
+  8.335 MF        1   10.97505    5.42183  531.23458    Glyoxylate                                        
+  9.925 FM        1   19.37573    3.36334  581.78554    Glycolate                                         
+ 13.462 BB        1   22.58038    2.65118  534.44585    Succinate                                         
+ 13.765 BB        1   27.60959    2.21601  546.21713    Glycerate                                         
+
+Totals without ISTD(s) :                  1.95262e4 
+
+1 Warnings or Errors :
+
+Warning : Calibration warnings (see calibration table listing)
+
+=====================================================================
+                          *** End of Report ***
diff -r 000000000000 -r 9072a2d2178b test-data/Report_Ex2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Report_Ex2.txt	Fri Oct 29 13:59:09 2021 +0000
@@ -0,0 +1,52 @@
+Data File C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\Std 500.D
+Sample Name: EX2
+MPSr-GCFID 10/19/2021 2:39:33 PM SYSTEM
+
+=====================================================================
+Acq. Operator   : SYSTEM                         Seq. Line :   8
+Sample Operator : SYSTEM                                                                     
+Acq. Instrument : MPSr-GCFID                      Location :   6  (F)
+Injection Date  : 10/11/2021 11:03:47 PM               Inj :   1
+                                                Inj Volume : 1 µl
+Acq. Method     : C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\190314_
+                  Glucides_prep_12-110.M
+Last changed    : 2/25/2021 3:02:59 PM by SYSTEM
+Analysis Method : C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\190314_
+                  Glucides_retraitement.M
+Last changed    : 10/19/2021 2:39:30 PM by SYSTEM
+                  (modified after loading)
+Additional Info : Peak(s) manually integrated
+=====================================================================
+                      Internal Standard Report                       
+=====================================================================
+
+Sorted By             :      Signal
+Calib. Data Modified  :      10/15/2021 5:02:32 PM
+Multiplier            :      1.0000
+Dilution              :      1.0000
+Sample Amount:        :    100.00000  [ng/ul]   (not used in calc.)
+Use Multiplier & Dilution Factor with ISTDs
+Sample ISTD Information:
+ISTD  ISTD Amount   Name
+  #    [ng/ul]  
+----|-------------|-------------------------
+  1    100.00000   Adonitol
+
+
+Signal 1: FID1 A, 
+
+RetTime  Type  ISTD    Area     Amt/Area    Amount   Grp   Name
+ [min]         used  [pA*s]      ratio     [ng/ul]  
+-------|------|----|----------|----------|----------|--|------------------
+ 18.803 FM   I    1   11.20124    1.00000  100.00000    Glyoxylate
+ 20.245 MF        1   33.88725    1.83246  554.37562    Glycolate
+ 21.196 FM        1   58.95049    1.03368  544.01047    Succinate
+ 21.483 BB        1   34.04986    1.80697  549.28838    Glycerate
+Totals without ISTD(s) :                  1.95262e4 
+
+1 Warnings or Errors :
+
+Warning : Calibration warnings (see calibration table listing)
+
+=====================================================================
+                          *** End of Report ***
diff -r 000000000000 -r 9072a2d2178b test-data/Report_Ex3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Report_Ex3.txt	Fri Oct 29 13:59:09 2021 +0000
@@ -0,0 +1,52 @@
+Data File C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\Std 500.D
+Sample Name: EX3
+MPSr-GCFID 10/19/2021 2:39:33 PM SYSTEM
+
+=====================================================================
+Acq. Operator   : SYSTEM                         Seq. Line :   8
+Sample Operator : SYSTEM                                                                     
+Acq. Instrument : MPSr-GCFID                      Location :   6  (F)
+Injection Date  : 10/11/2021 11:03:47 PM               Inj :   1
+                                                Inj Volume : 1 µl
+Acq. Method     : C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\190314_
+                  Glucides_prep_12-110.M
+Last changed    : 2/25/2021 3:02:59 PM by SYSTEM
+Analysis Method : C:\Chemstation\1\Data\211011_Corentin-Younes 2021-10-11 15-56-48\190314_
+                  Glucides_retraitement.M
+Last changed    : 10/19/2021 2:39:30 PM by SYSTEM
+                  (modified after loading)
+Additional Info : Peak(s) manually integrated
+=====================================================================
+                      Internal Standard Report                       
+=====================================================================
+
+Sorted By             :      Signal
+Calib. Data Modified  :      10/15/2021 5:02:32 PM
+Multiplier            :      1.0000
+Dilution              :      1.0000
+Sample Amount:        :    100.00000  [ng/ul]   (not used in calc.)
+Use Multiplier & Dilution Factor with ISTDs
+Sample ISTD Information:
+ISTD  ISTD Amount   Name
+  #    [ng/ul]  
+----|-------------|-------------------------
+  1    100.00000   Adonitol
+
+
+Signal 1: FID1 A, 
+
+RetTime  Type  ISTD    Area     Amt/Area    Amount   Grp   Name
+ [min]         used  [pA*s]      ratio     [ng/ul]  
+-------|------|----|----------|----------|----------|--|------------------
+ 35.470 MF        1   13.78376    4.35693  536.14458    Glyoxylate
+ 36.658 MF        1   44.91168    1.35313  542.53994    Glycolate
+ 41.559 MF        1  110.09505 5.54692e-1  545.19732    Succinate
+ 42.896 MF        1  158.98767 3.54025e-1  502.49442    Glycerate
+Totals without ISTD(s) :                  1.95262e4 
+
+1 Warnings or Errors :
+
+Warning : Calibration warnings (see calibration table listing)
+
+=====================================================================
+                          *** End of Report ***
diff -r 000000000000 -r 9072a2d2178b test-data/Results.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Results.csv	Fri Oct 29 13:59:09 2021 +0000
@@ -0,0 +1,4 @@
+;Glyoxylate;Glycolate;Succinate;Glycerate
+EX1;10.97505;19.37573;22.58038;27.60959;
+EX2;11.20124;33.88725;58.95049;34.04986;
+EX3;13.78376;44.91168;110.09505;158.98767;