Metams

tools/metams/.shed.yml

@@ -0,0 +1,39 @@
+definitions:
+  include: &default-includes
+    - test-data
+    - static
+    - lib.r
+    - macros.xml
+
+name: metams
+owner: workflow4metabolomics
+remote_repository_url: https://github.com/workflow4metabolomics/tools-metabolomics/
+homepage_url: http://workflow4metabolomics.org
+categories:
+- Metabolomics
+
+repositories:
+  metams_plot:
+    description: '[Metabolomics][W4M][GC-MS] GC-MS plotting after data preprocessing using metaMS package'
+    long_description: |
+      Part of the W4M project : http://workflow4metabolomics.org Plotting of preprocessing data by metaMS.
+    owner: workflow4metabolomics
+    include:
+      [*default-includes, metams_plot.xml, metams_plot.r]
+  metams_run_gc:
+    description: '[Metabolomics][W4M][GC-MS] metaMS R Package - GC-MS data preprocessing using metaMS package'
+    long_description: |
+      Part of the W4M project: http://workflow4metabolomics.org 
+      metaMS: https://www.bioconductor.org/packages/release/bioc/html/metaMS.html MS-based metabolomics data processing and compound annotation pipeline.
+    owner: yguitton
+    include:
+      [*default-includes, metams_run_gc.xml, metams_run_gc.r]
+
+suite:
+  name: suite_metams
+  owner: workflow4metabolomics
+  homepage_url: http://workflow4metabolomics.org
+  description: '[Metabolomics][W4M][GC-MS] metaMS R package - GC-MS data preprocessing using metaMS package and plotting on these datas'
+  long_description: |
+    Part of the W4M project : http://workflow4metabolomics.org 
+    metaMS: https://www.bioconductor.org/packages/release/bioc/html/metaMS.html MS-based metabolomics data processing, compound annotation pipeline and plotting.

tools/metams/README.rst

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+====================================
+GC-MS data processing version 2.1.1
+====================================
+
+1) Date : 2019-05-20
+
+2) Author and maintainer :
+
+   Yann GUITTON
+
+   LABERCA - PFCA Metabolomics Platform
+
+   E-mail: [email protected] / [email protected]
+
+3) Funding :
+
+   Developed within IDEALG project (http://www.idealg.ueb.eu/versionAnglaise/)
+
+   Developed within IFB-MetaboHub W4M project
+
+4) Usage restrictions :
+
+   Use of this tool is restricted to the service conditions of the MetaboHUB-IFB infrastructures.
+   For any question regarding the use of these services, please contact: [email protected]
+
+5) Installation :
+
+   4 files are required for installation :
+
+   - 'README.rst'
+         Instructions for installation
+
+   - 'metaMS_plot.xml'
+         Configuration file; to be put into the './galaxy-dist/tools/' directory 
+         and 2.png files for illustration
+
+   - 'metaMS_plot.r'
+         Wrapper code written in R aimed at launching the runGC function from the metaMS package given the arguments entered by the user through the Galaxy interface
+
+   - 'metaMS R package '
+         The 'metaMS' package requires dependencies and can be installed with source("http://bioconductor.org/biocLite.R") or `biocLite("metaMS")`
+
+         This code is for installation of the Galaxy module on the Workflow4metabolomics.org MetaboHUB-IFB platform only and must not be distributed without the author agreement
+
+
+Changelog/News
+--------------
+**Version 1.0 - 20/05/2019**
+
+- NEW : new tool extract from previous metaMS_runGC tool. EICs have been corrected.
+
+Test Status
+-----------
+
+Planemo test using conda: passed
+
+
+====================================
+GC-MS data processing version 3.0.0
+====================================
+
+1) Date : 2019-05-20
+
+2) Author and maintainer :
+
+   Yann GUITTON
+
+   LABERCA - PFCA Metabolomics Platform
+
+   E-mail: [email protected] / [email protected]
+
+3) Funding :
+
+   Developed within IDEALG project (http://www.idealg.ueb.eu/versionAnglaise/)
+
+   Developed within IFB-MetaboHub W4M project
+
+4) Usage restrictions :
+
+   Use of this tool is restricted to the service conditions of the MetaboHUB-IFB infrastructures.
+   For any question regarding the use of these services, please contact: [email protected]
+
+5) Installation :
+
+   4 files are required for installation :
+
+   - 'README.rst'
+         Instructions for installation
+
+   - 'metaMS_runGC.xml'
+         Configuration file; to be put into the './galaxy-dist/tools/' directory 
+         and 2.png files for illustration
+
+   - 'metaMS_runGC.r'
+         Wrapper code written in R aimed at launching the runGC function from the metaMS package given the arguments entered by the user through the Galaxy interface
+
+   - 'metaMS R package '
+         The 'metaMS' package requires dependencies and can be installed with source("http://bioconductor.org/biocLite.R") or `biocLite("metaMS")`
+
+         This code is for installation of the Galaxy module on the Workflow4metabolomics.org MetaboHUB-IFB platform only and must not be distributed without the author agreement
+
+
+Changelog/News
+--------------
+**Version 3.0 - 20/05/2019**
+
+- Divided tool into two new. One will be metaMS_plot and this one stay the same without plotting chromatograms and without zip files
+
+**Version 2.0 - 15/05/2017**
+
+- RI option, better usage of ri filter and easier file reading for RI database
+
+**Version 1.1 - 11/07/2016**
+
+- TEST: refactoring to pass planemo test using conda dependencies
+
+**Version 1.0 - 01/06/2015**
+
+- NEW: new tool
+
+Test Status
+-----------
+
+Planemo test using conda: passed