0.1.6 release (#28)

* udpate Readme and plugin gpg https://github.com/jodersky/sbt-gpg * downgrade gpg to 0.2.1. 0.2.2 not available ! * remove tagret directory fro repo * remove tagret directory fro repo * update Readme * fix jar publication * covered code for commands * update readme with badge * remove script * change galaxy recipe directory * remove temp file * minor fix for resume * add planemo test * add planemo test * add planemo test * add planemo test * add planemo test * planemo test only master/main/develop * lint planemo + conda test version * lint planemo + conda test version * lint planemo + conda test version * update fix meta.yml * remove conda recipe * clean repo * add sbt-release (#16) * Sbt release (#18) * add sbt-release * valid pom generation * Dockerfile (#20) * target directory for assembly * add dockerized task * add dockerfile * update gitignore * use directory docker * update docker management * fix outputdir assembly * update docker config * remove debug config * Dockerfile (#22) * target directory for assembly * add dockerized task * add dockerfile * update gitignore * use directory docker * update docker management * fix outputdir assembly * update docker config * remove debug config * remove coverage enable * fix dockerfile implementation to run process inside galaxy tools * Uplc tqd to isocor 24 (#26) * update Readme * add MassLynx parser / tests * replace strip with trim * increase coverage. manage bad line def inside array compound * fix coverage * fix coverage * add command/output object and tests * save notes * add galaxy config tools - gcms2isocor openlabcds2csv masslynx2isocor (#27) * add galaxy config tools - gcms2isocor openlabcds2csv masslynx2isocor * fix doc/name bin * downgrade profile galaxy version * fx test masslynx
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diff --git a/README.md b/README.md
@@ -4,23 +4,44 @@
 [![codecov](https://codecov.io/gh/p2m2/p2m2tools/branch/develop/graph/badge.svg)](https://codecov.io/gh/p2m2/p2m2)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/9db61bd9732740c79a39de678c6e5246)](https://www.codacy.com/gh/p2m2/p2m2tools/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=p2m2/p2m2tools&amp;utm_campaign=Badge_Grade)
 
-Development of bioinformatics tools/software related to P2M2 platform activities.
+Development of bioinformatics tools/software related to P2M2 platform (IGEPP's Metabolic Profiling and Metabolomic Platform) activities.
 All the tools developed are accessible via the Galaxy instance of the Genouest platform (https://galaxy.genouest.org/)
 
 ## GCMS2Isocor
 
 Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs.
-A P2M2 (IGEPP's Metabolic Profiling and Metabolomic Platform) workflow was built to obtain carbon isotopologue distribution of specific metabolites (complete list of metabolites available in the file "Metabolite.dat") from GC-MS raw data files. The input files for this workflow can be any GC-MS raw dataset that contains a column "Name" filled with each carbon isotopologue of each fragment considered and a column "Area" filled with the area of the integrated peak. The name of each fragment must be written exactly as specified in the "Metabolite.dat" file to ensure accurate correction with IsoCor. Example: the name "ProlineC2C5_TMS_m0" is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146). (2021-10-17) (2021-10-17)
+A P2M2  workflow was built to obtain carbon isotopologue distribution of specific metabolites (complete list of metabolites available in the file "Metabolite.dat") from GC-MS raw data files. The input files for this workflow can be any GC-MS raw dataset that contains a column "Name" filled with each carbon isotopologue of each fragment considered and a column "Area" filled with the area of the integrated peak. The name of each fragment must be written exactly as specified in the "Metabolite.dat" file to ensure accurate correction with IsoCor. Example: the name "ProlineC2C5_TMS_m0" is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146). (2021-10-17) (2021-10-17)
 https://doi.org/10.15454/1I9PET
 
 [Galaxy worklow](https://galaxy.genouest.org/u/ofilangi-1/w/corrective-method-dedicated-to-isocor-for-calculating-carbon-isotopologue-distribution-from-gcms-runs-5)
 
+### Targeted P2M2 device
+
+| **Manufacturer** | **Model**     |
+|-----------------|---------------| 
+| GCMS Shimadzu   | GCTQD (TQ8040) |
+
+
 
 ## OpenLabCds2Csv
 
 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)
-
 
+### Targeted P2M2 device
+
+| **Manufacturer** | **Model**            |
+|----------------|----------------------| 
+| Agilent        | GC-FID Agilent 6890N |
+
+## MassLynx2Isocor
+
+Build Isocor input file from MassLynx report ("Quantify Compound Summary Report") 
+
+### Targeted P2M2 device
+
+| **Manufacturer** | **Model**        |
+|-----------------|------------------| 
+| Waters Acquity  | HPLC TQD         |
 
 
diff --git a/README_dev.md b/README_dev.md
@@ -5,11 +5,16 @@ sbt assembly
 ```
 ### Tools
 
+```shell
+JAR=assembly/$(ls  assembly/ | tail -n1)
+```
+
 ### Gcms2Isocor
 
-``` 
-./gcms2isocor --help
-./gcms2isocor src/test/resources/GCMS/13CPROT1.txt src/test/resources/GCMS/13CPROT2.txt --out input_isocor.tsv
+```
+COMMAND="fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand"
+java -cp $JAR $COMMAND --help
+java -cp $JAR $COMMAND src/test/resources/GCMS/13CPROT1.txt src/test/resources/GCMS/13CPROT2.txt --out input_isocor.tsv
 ```
 
 ### Input Data / GCMS PostRun Analysis
@@ -25,8 +30,17 @@ name -> extraire (metabolite/derivative/isotologue)
 ### OpenLabCDS2Csv
 
 ```
-./openLabCds2Csv --help
-./openLabCds2Csv src/test/resources/OpenLabCDS/Report_Ex1.txt src/test/resources/OpenLabCDS/Report_Ex2.txt src/test/resources/OpenLabCDS/Report_Ex3.txt --out text.csv
+COMMAND="fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand"
+java -cp $JAR $COMMAND --help
+java -cp $JAR $COMMAND src/test/resources/OpenLabCDS/Report_Ex1.txt src/test/resources/OpenLabCDS/Report_Ex2.txt src/test/resources/OpenLabCDS/Report_Ex3.txt --out text.csv
+```
+
+### 
+
+```
+COMMAND="fr.inrae.metabolomics.p2m2.command.MassLynx2IsocorCommand"
+java -cp $JAR $COMMAND --help
+java -cp $JAR $COMMAND src/test/resources/MassLynx/mass_15Ngly.txt -d src/test/resources/MassLynx/correspondence_derivatives.txt --out input_isocor.tsv
 ```
 
 ## Create conda package
@@ -52,6 +66,7 @@ p2m2tools fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand --help
 
 - fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand
 - fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand
+- fr.inrae.metabolomics.p2m2.command.MassLynx2IsocorCommand
 
 ## circle-ci
 

diff --git a/README_genostack_galaxytest.md b/README_genostack_galaxytest.md
@@ -2,13 +2,27 @@
 
 https://galaxy-p2m2-192-168-100-198.vm.openstack.genouest.org/
 
+## VM configuration
+
+Debian 10.10
+
+```shell
+ssh [email protected]
+```
+## config genouest
+
+si *test-galaxy* est le nom de la machine
+``` 
+dans /etc/hosts
+127.0.0.1 test-galaxy
+```
 
 ## mount directory
 
 - doc : https://www.genouest.org/outils/genostack/volumes.html
 - /mnt/galaxy
 
-```
+```shell
 sudo -i
 lsblk -f
 mkfs.ext4 /dev/vdb
@@ -21,7 +35,7 @@ mount /dev/vdb /mnt/galaxy
 
 see https://github.com/bgruening/docker-galaxy-stable
 
-```
+```shell
 cd /mnt/galaxy
 git clone https://github.com/bgruening/docker-galaxy-stable.git
 ```
@@ -35,15 +49,15 @@ git clone https://github.com/bgruening/docker-galaxy-stable.git
 ## config (ADMIN_USER,....)
 
 
-```
+```shell
 cp /mnt/galaxy/docker-galaxy-stable/compose/docker-compose.yml docker-compose.yml 
 vi docker-compose.yml 
 cp docker-compose.yml /mnt/galaxy/docker-galaxy-stable/compose/
 ```
 
 
 ### run galaxy
-```
+```shell
 cd /mnt/galaxy/docker-galaxy-stable/compose/
 docker-compose up -d
 ```
@@ -55,15 +69,28 @@ docker-compose up -d
 
 #### copy tool
 
-`sudo cp -r /home/debian/MetabolomicsWorkflowTools/galaxy/gcms2isocor /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/tools/
+`sudo cp -r /home/debian/p2m2tools/galaxy/gcms2isocor /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/tools/
 
 ### add tool menu 
 if tool_conf.xml exist : 
 `cp tool_conf.xml /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/config/`
 
-or add section in `/mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/config/tool_conf.xml`
+or create `/mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/config/tool_conf.xml`
 ```
-<section name="Metabolomics" id="metabolomics">
-	  <tool file="gcms2isocor/gcms2isocor.xml" />
+<?xml version="1.0"?>
+<toolbox>
+  <section name="Metabolomics" id="metabolomics">
+        <tool file="gcms2isocor/gcms2isocor.xml" />
   </section>
+
+ <section name="Metabolomics" id="metabolomics">
+        <tool file="openlabcds2csv/openlabcds2csv.xml" />
+ </section>
+
+
+ <section name="Metabolomics" id="metabolomics">
+     <tool file="masslynx2isocor/masslynx2isocor.xml" />
+ </section>
+
+</toolbox>
 ```
diff --git a/build.sbt b/build.sbt
@@ -16,7 +16,7 @@ scmInfo := Some(
 
 versionScheme := Some("early-semver")
 
-val static_version      = "0.1.5"
+val static_version      = "0.1.6"
 val version_build = scala.util.Properties.envOrElse("PROG_VERSION", static_version )
 
 version :=  version_build

diff --git a/galaxy/README.md b/galaxy/README.md
@@ -0,0 +1,5 @@
+# Depot Galaxy
+
+## Planemo test
+
+```planemo -t```
diff --git a/galaxy/docker_env_exemple/.shed.yml b/galaxy/docker_env_exemple/.shed.yml
@@ -0,0 +1,4 @@
+categories: [Metabolomics]
+description: Conversion from GCMS PostRun Analysis to Isocor
+name: gcms2isocor
+owner: genouest
diff --git a/galaxy/docker_env_exemple/README.md b/galaxy/docker_env_exemple/README.md
@@ -0,0 +1,11 @@
+### dev notes
+
+## repo
+
+https://github.com/p2m2/p2m2tools
+
+## planemo
+
+planemo l --report_level error
+planemo t --docker
+
diff --git a/galaxy/docker_env_exemple/gcms2isocor.xml b/galaxy/docker_env_exemple/gcms2isocor.xml
@@ -0,0 +1,39 @@
+<tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" version="1.0.0">
+    <requirements>	
+        <container type="docker">inraep2m2/p2m2tools:0.1.5</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      p2m2tools fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand 
+       #for $input in $input_gcms_files
+         #if $input
+           $input
+         #end if
+        #end for
+        --out '$output_isocor'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_gcms_files" multiple="true" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="output_isocor" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/>
+            <output name="output_isocor" file="input_isocor.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Convert the GC-MS raw data input files into a unique table suitable as input file for IsoCor.
+	
+	Processes GCMS files should be exported with the following categories: [Header], [MS Quantitative Results].
+	GC-MS raw dataset should contains a column "Name" filled with each carbon isotopologue of each fragment considered and a column "Area" filled with the area of the integrated peak. 
+	The name of each fragment must be written exactly as specified in the "Metabolite.dat" file (see https://isocor.readthedocs.io/en/latest/tutorials.html#input-data) to ensure accurate correction with
+	IsoCor. 
+
+	Example: the name “ProlineC2C5_TMS_m0” is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue
+	monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146).
+
+    Questions, suggestions or bugs report, please submit an issue at https://github.com/p2m2/p2m2tools/issues/new?labels=bug&title=[GCMS2IsocorCommand].
+    ]]></help>
+</tool>