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Metams#275

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lecorguille wants to merge 206 commits intomasterworkflow4metabolomics/tools-metabolomics:masterfrom metamsworkflow4metabolomics/tools-metabolomics:metamsCopy head branch name to clipboard

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Commits on May 22, 2016

• first commit

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• Update README.md

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• first commit

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• Update README.md

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• Create .shed.yml

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• Create test.txt

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• still erros

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• Create tool_dependencies.xml

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Commits on Jul 5, 2016

• Update README.md

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Commits on Jul 10, 2016

• Merge pull request #1 from workflow4metabolomics/lecorguille-fix-doc

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Commits on Jul 11, 2016

• first commit

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• cosmetic changes

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• conda OK ; planemo OK

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• add doc

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• Merge pull request #2 from workflow4metabolomics/dev_planemo_conda

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• planemo lint

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• rename the tool

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Commits on Jul 12, 2016

• Textual Details for RI option + YGU email update

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Commits on Jul 13, 2016

• add some test-data

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• Update metams_runGC.xml

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Commits on Jul 28, 2016

• Add Metabolomics tag in Galaxy toolshed descriptions.

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• Update .travis.yml

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• Merge pull request #7 from workflow4metabolomics/dev-toolshed

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Commits on Sep 5, 2016

• Add credit to Ralf for base script

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Commits on Sep 8, 2016

• Bug correction in plotUnknown if no peak found

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• version update after bug correction

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Commits on Apr 13, 2017

• add make.names in sampleMetadata

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Commits on Apr 25, 2017

• try to solve travis error

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Commits on May 10, 2017

• Travis update

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Commits on May 15, 2017

• new files test-data all default

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• version 2.0 with RI filter

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• version 2.0 update

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Commits on May 19, 2017

• New version 2.0 with RI search modified

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• Merge pull request #16 from workflow4metabolomics/fix_travis

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Commits on May 30, 2017

• add relative link management functions

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Commits on Jun 2, 2017

• add minutes or seconds to title, add none option to plotUnknowns

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• Add try to plotUnknown if error generate empty pdf

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Commits on Oct 16, 2017

• update to 2.1.1 as in production

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Commits on Nov 8, 2017

• add make.names in sampleMetadata

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• Add files via upload

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Commits on Feb 16, 2018

• increase planemo and galaxy version in travis tests

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Commits on Mar 2, 2018

• Update metams_runGC.xml

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Commits on Sep 18, 2018

• Update metams_runGC.xml

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• Update metams_runGC.xml

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Commits on Oct 10, 2018

• Merge pull request #24 from workflow4metabolomics/fix_tarvis2

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Commits on May 20, 2019

• Remake tree files

  

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• add travis and git files

  

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• Add metaMS_plot

  

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• Rename macros

  

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• update test files

  

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• update file metaMS_runGC

  

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• adapt symlink tests

  

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Commits on May 21, 2019

• Modify R script for runGC

  

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• Revert "Modify R script for runGC"

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• Update R script for runGC

  

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• Rename file

  

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• Update xml runGC file

  

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• Update tests runGC

  

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• Update README runGC

  

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• Change path for lib and macro symlinks

  

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• Update lib.r

  

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• Correct one mistake

  

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• Change little travis test

  

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• update tests plot

  

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• little change

  

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• update readmes

  

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Commits on May 22, 2019

• change indentation

  

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• little fix

  

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• fix

  

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• update readme

  

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Commits on Jun 3, 2019

• few reviews

  

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• correct indentation

  

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• modify tests conditionals

  

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• delete log file

  

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• resolve indentation

  

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• try test

  

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• add conda

  

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• modify GS

  

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• try GS

  

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Commits on Jun 4, 2019

• adapt test datas

  

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• modify name

  

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• modify name

  

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• update tests

  

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• change name

  

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• update tests

  

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• Remake tree files

  

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• add travis and git files

  

  jsaintvanne

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• Add metaMS_plot

  

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• Rename macros

  

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• update test files

  

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• update file metaMS_runGC

  

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• adapt symlink tests

  

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• Modify R script for runGC

  

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• Revert "Modify R script for runGC"

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• Update R script for runGC

  

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• Rename file

  

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• Update xml runGC file

  

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• Update tests runGC

  

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• Update README runGC

  

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• Change path for lib and macro symlinks

  

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• Update lib.r

  

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• Correct one mistake

  

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• Change little travis test

  

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• update tests plot

  

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• little change

  

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• update readmes

  

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• change indentation

  

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• little fix

  

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• fix

  

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• update readme

  

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• few reviews

  

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• correct indentation

  

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• modify tests conditionals

  

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• delete log file

  

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• resolve indentation

  

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• try test

  

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• add conda

  

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• modify GS

  

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• try GS

  

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• adapt test datas

  

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• modify name

  

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• modify name

  

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• update tests

  

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• change name

  

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• update tests

  

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• adjust

  

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• some changes

  

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• try update tests

  

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• delete log files

  

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Commits on Jun 5, 2019

• try pictures

  

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• try gs test

  

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• update shebang, tests plot

  

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Commits on Jun 12, 2019

• add gs in xml

  

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• delete gs in travis

  

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• Merge pull request #29 from jsaintvanne/fix_zip

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• change owner metams_rungc

  

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• change owner shed

  

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Commits on Jun 13, 2019

• some readme

  

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• change id

  

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• just a change

  

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Commits on Jun 14, 2019

• change names

  

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• Merge pull request #32 from jsaintvanne/fix_zip

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Commits on Jul 16, 2019

• add warning for cdf issue

  

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Commits on Jul 17, 2019

• Correction for TIC and BPC from cdf files

  

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Commits on Aug 12, 2019

• corection when 1 file

  

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Commits on Aug 13, 2019

• some changes

  

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Commits on Aug 20, 2019

• change data test

  

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Commits on Aug 21, 2019

• change

  

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• change data test after change DB a little

  

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• add to delete

  

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• wrong branch

  

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• wrong branch

  

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• correction changes

  

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• update data tests

  

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• update tests

  

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Commits on Sep 2, 2019

• Merge pull request #35 from jsaintvanne/correct1file

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Commits on Sep 3, 2019

• Merge branch 'dev' into dev

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• unpdate BPC

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• Merge pull request #38 from jsaintvanne/dev

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• add warning for CDF and result null correction

  

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• delete correct null result

  

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Commits on Sep 5, 2019

• Merge pull request #41 from jsaintvanne/dev

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Commits on Nov 5, 2019

• change pictures

  

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Commits on Jan 27, 2020

• delete fwhm

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• delete fwhm param

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• Merge pull request #43 from jsaintvanne/dev

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Commits on Apr 28, 2020

• change metams version

  

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• change rbatch version

  

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Commits on Apr 29, 2020

• versionning with macro

  

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• corrections for versionning

  

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Commits on Apr 30, 2020

• correction of double space in DB

  

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• move authors and citations as macros

  

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• change authors and citations with macro

  

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• correction of double spaces again

  

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Commits on May 6, 2020

• update runGC test data

  

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• update macro authors for planemo lint

  

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• put TODO in an isue

  

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• Merge pull request #45 from jsaintvanne/dev

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Commits on Jun 18, 2020

• Full remove of fwhmparam not needed anymore

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Commits on Jun 26, 2020

• Merge pull request #47 from workflow4metabolomics/dev.fwhmparam

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Commits on Jul 2, 2020

• tool version update

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Commits on Jul 15, 2020

• Update macro.xml to use metaMS R package version 1.24.0

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  0030bc9

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• change Travis branch target to dev

  yguitton

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  da591ff

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Commits on Feb 13, 2022

• Update version

  gallardoalba

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  5f41ab4

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Commits on Feb 14, 2022

• Merge pull request #50 from gallardoalba/Update_metaMS_version

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  yguitton

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  0f4e17c

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Commits on Oct 6, 2024

• Prep migration

  lecorguille

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  4444c59

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• Merge remote-tracking branch 'metams/prep_migration'

  lecorguille

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  8a10f2a

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Commits on Oct 8, 2024

• change links in help section of runGC tool for lint errors

  jsaintvanne

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  7d9c621

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• change links in help section of runGC tool for lint errors second test

  jsaintvanne

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  b9aeb59

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• change version name

  jsaintvanne

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  e9a0367

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• change version name test 2

  jsaintvanne

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  fd571f0

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• correct test of plot tool with expect_num_outputs

  jsaintvanne

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  65568c2

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Commits on Oct 9, 2024

• mv metams in tools folder

  lecorguille

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  d3b6bd2

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Commits on Oct 23, 2024

• Try to correct the indentation problem with lintr

  DamienCode404

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  217570f

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• Lintr error corrections

  DamienCode404

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  0f42d95

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• Lintr : Commented code should be removed.

  DamienCode404

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  bc6be48

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Commits on Nov 8, 2024

• fix: Test input file cannot be found.

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  DamienCode404

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  ae422d3

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• refactor: Change of structure for metams tool

  DamienCode404

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  7d8000d

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Commits on Nov 13, 2024

• refactor: change test files (>1M) and update code base

  DamienCode404

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  6c7f5fe

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Commits on Nov 14, 2024

• Fix: Rename file with lower-case character

  DamienCode404

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  c2ba93e

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• fix: Tool version with PEP 440

  DamienCode404

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  aa882ad

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• fix: Tool versioning

  DamienCode404

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  c284f8f

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• test-data: rungc

  DamienCode404

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  769e93d

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• test-data: metams_plot

  DamienCode404

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  5274459

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• fix: try with no single string in command rscript

  DamienCode404

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  16ec8dd

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• fix: change name file

  DamienCode404

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  b56771e

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