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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

+60,549

Commits

Commits on May 22, 2016

• first commit

  yguitton

  committed
  dda8940

• Update README.md

  yguitton

  committed
  a6fba2a

• first commit

  yguitton

  committed
  3c2f1fe

• Update README.md

  yguitton

  committed
  d6abb85

• Create .shed.yml

  yguitton

  committed
  4a88b69

• Create test.txt

  yguitton

  committed
  8406bdc

• still erros

  yguitton

  committed
  5632815

• Create tool_dependencies.xml

  yguitton

  committed
  867bc2b

Commits on Jul 5, 2016

• Update README.md

  Show description for 85a3ef4
  lecorguille

  authored
  85a3ef4

Commits on Jul 10, 2016

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

  Show description for a9fd8f3
  lecorguille

  authored
  a9fd8f3

Commits on Jul 11, 2016

• first commit

  yguitton

  committed
  b2bede5

• cosmetic changes

  lecorguille

  committed
  bcbc6d7

• conda OK ; planemo OK

  lecorguille

  committed
  5750f1a

• add doc

  lecorguille

  committed
  a9ec218

• Merge pull request #2 from workflow4metabolomics/dev_planemo_conda

  Show description for 99ea2b3
  lecorguille

  authored
  99ea2b3

• planemo lint

  lecorguille

  committed
  08d5de9

• rename the tool

  lecorguille

  committed
  f5df117

Commits on Jul 12, 2016

• Textual Details for RI option + YGU email update

  yguitton

  authored
  5e5a18b

Commits on Jul 13, 2016

• add some test-data

  lecorguille

  committed
  5a49c17

• Update metams_runGC.xml

  Show description for 6384fcf
  lecorguille

  authored
  6384fcf

Commits on Jul 28, 2016

• Add Metabolomics tag in Galaxy toolshed descriptions.

  pkrog

  committed
  d3ed8ce

• Update .travis.yml

  Show description for f6cc2c6
  lecorguille

  authored
  f6cc2c6

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

  Show description for a47dbc8
  lecorguille

  authored
  a47dbc8

Commits on Sep 5, 2016

• Add credit to Ralf for base script

  yguitton

  authored
  abce9a2

Commits on Sep 8, 2016

• Bug correction in plotUnknown if no peak found

  Show description for e86b491
  yguitton

  authored
  e86b491

• version update after bug correction

  yguitton

  authored
  006eacc

Commits on Apr 13, 2017

• add make.names in sampleMetadata

  Show description for 720c352
  yguitton

  authored
  720c352

Commits on Apr 25, 2017

• try to solve travis error

  yguitton

  authored
  18e0d03

Commits on May 10, 2017

• Travis update

  lecorguille

  committed
  c7ff5c2

Commits on May 15, 2017

• new files test-data all default

  yguitton

  authored
  2c0900d

• version 2.0 with RI filter

  yguitton

  authored
  56f80e2

• version 2.0 update

  yguitton

  authored
  da81a1b

Commits on May 19, 2017

• New version 2.0 with RI search modified

  yguitton

  authored
  d282d0e

• Merge pull request #16 from workflow4metabolomics/fix_travis

  Show description for 8bbbd8e
  yguitton

  authored
  8bbbd8e

Commits on May 30, 2017

• add relative link management functions

  yguitton

  authored
  e64fd8e

Commits on Jun 2, 2017

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

  yguitton

  authored
  be48065

• Add try to plotUnknown if error generate empty pdf

  yguitton

  authored
  0b816a8

Commits on Oct 16, 2017

• update to 2.1.1 as in production

  yguitton

  authored
  71038a1

Commits on Nov 8, 2017

• add make.names in sampleMetadata

  yguitton

  authored
  a69ca6d

• Add files via upload

  yguitton

  authored
  d14f40d

Commits on Feb 16, 2018

• increase planemo and galaxy version in travis tests

  lecorguille

  committed
  5324fcb

Commits on Mar 2, 2018

• Update metams_runGC.xml

  Show description for fa0896f
  lecorguille

  authored
  fa0896f

Commits on Sep 18, 2018

• Update metams_runGC.xml

  lecorguille

  authored
  12635dd

• Update metams_runGC.xml

  lecorguille

  authored
  074e7f4

Commits on Oct 10, 2018

• Merge pull request #24 from workflow4metabolomics/fix_tarvis2

  Show description for d55838e
  lecorguille

  authored
  d55838e

Commits on May 20, 2019

• Remake tree files

  

  jsaintvanne

  committed
  e9f7761

• add travis and git files

  

  jsaintvanne

  committed
  024b2c9

• Add metaMS_plot

  

  jsaintvanne

  committed
  782ede9

• Rename macros

  

  jsaintvanne

  committed
  2fd65c6

• update test files

  

  jsaintvanne

  committed
  13d25a6

• update file metaMS_runGC

  

  jsaintvanne

  committed
  62c9f54

• adapt symlink tests

  

  jsaintvanne

  committed
  20a2c85

Commits on May 21, 2019

• Modify R script for runGC

  

  jsaintvanne

  committed
  d28c776

• Revert "Modify R script for runGC"

  Show description for 5c1d240
  

  jsaintvanne

  committed
  5c1d240

• Update R script for runGC

  

  jsaintvanne

  committed
  3b9b47e

• Rename file

  

  jsaintvanne

  committed
  b4b9915

• Update xml runGC file

  

  jsaintvanne

  committed
  d596199

• Update tests runGC

  

  jsaintvanne

  committed
  3768ea7

• Update README runGC

  

  jsaintvanne

  committed
  0103a37

• Change path for lib and macro symlinks

  

  jsaintvanne

  committed
  d98cd8c

• Update lib.r

  

  jsaintvanne

  committed
  b2060ff

• Correct one mistake

  

  jsaintvanne

  committed
  6737e29

• Change little travis test

  

  jsaintvanne

  committed
  7fc96f8

• update tests plot

  

  jsaintvanne

  committed
  ee18ff5

• little change

  

  jsaintvanne

  committed
  b782f4f

• update readmes

  

  jsaintvanne

  committed
  776286f

Commits on May 22, 2019

• change indentation

  

  jsaintvanne

  committed
  c10088c

• little fix

  

  jsaintvanne

  committed
  f4fc151

• fix

  

  jsaintvanne

  committed
  74e0b52

• update readme

  

  jsaintvanne

  committed
  f3ae47a

Commits on Jun 3, 2019

• few reviews

  

  jsaintvanne

  committed
  b90b7fe

• correct indentation

  

  jsaintvanne

  committed
  6bf0c30

• modify tests conditionals

  

  jsaintvanne

  committed
  71d71ef

• delete log file

  

  jsaintvanne

  committed
  1f843e3

• resolve indentation

  

  jsaintvanne

  committed
  b025b15

• try test

  

  jsaintvanne

  committed
  ed29d32

• add conda

  

  jsaintvanne

  committed
  32612f9

• modify GS

  

  jsaintvanne

  committed
  90a5856

• try GS

  

  jsaintvanne

  committed
  b021188

Commits on Jun 4, 2019

• adapt test datas

  

  jsaintvanne

  committed
  2f3e59f

• modify name

  

  jsaintvanne

  committed
  737a14a

• modify name

  

  jsaintvanne

  committed
  19012b4

• update tests

  

  jsaintvanne

  committed
  3a0b030

• change name

  

  jsaintvanne

  committed
  12dee9f

• update tests

  

  jsaintvanne

  committed
  0ac2fb8

• Remake tree files

  

  jsaintvanne

  committed
  107c0dd

• add travis and git files

  

  jsaintvanne

  committed
  3f7a8cc

• Add metaMS_plot

  

  jsaintvanne

  committed
  15d62b1

• Rename macros

  

  jsaintvanne

  committed
  f8482ee

• update test files

  

  jsaintvanne

  committed
  e5d1fb0

• update file metaMS_runGC

  

  jsaintvanne

  committed
  285d673

• adapt symlink tests

  

  jsaintvanne

  committed
  adb4f83

• Modify R script for runGC

  

  jsaintvanne

  committed
  ca79779

• Revert "Modify R script for runGC"

  Show description for 012d49b
  

  jsaintvanne

  committed
  012d49b

• Update R script for runGC

  

  jsaintvanne

  committed
  6cab746

• Rename file

  

  jsaintvanne

  committed
  b4b4258

• Update xml runGC file

  

  jsaintvanne

  committed
  d996f6c

• Update tests runGC

  

  jsaintvanne

  committed
  b6cde76

• Update README runGC

  

  jsaintvanne

  committed
  c1f4900

• Change path for lib and macro symlinks

  

  jsaintvanne

  committed
  6ebd725

• Update lib.r

  

  jsaintvanne

  committed
  52fcdd5

• Correct one mistake

  

  jsaintvanne

  committed
  db83b13

• Change little travis test

  

  jsaintvanne

  committed
  948e26c

• update tests plot

  

  jsaintvanne

  committed
  5279b82

• little change

  

  jsaintvanne

  committed
  89eaaed

• update readmes

  

  jsaintvanne

  committed
  5f3a525

• change indentation

  

  jsaintvanne

  committed
  1f64d0c

• little fix

  

  jsaintvanne

  committed
  14f90b0

• fix

  

  jsaintvanne

  committed
  0b45662

• update readme

  

  jsaintvanne

  committed
  5870cf7

• few reviews

  

  jsaintvanne

  committed
  2566d5d

• correct indentation

  

  jsaintvanne

  committed
  08d4675

• modify tests conditionals

  

  jsaintvanne

  committed
  f7c768c

• delete log file

  

  jsaintvanne

  committed
  7df4e9e

• resolve indentation

  

  jsaintvanne

  committed
  1080698

• try test

  

  jsaintvanne

  committed
  c78e3e3

• add conda

  

  jsaintvanne

  committed
  a323b29

• modify GS

  

  jsaintvanne

  committed
  5d59cdf

• try GS

  

  jsaintvanne

  committed
  a432378

• adapt test datas

  

  jsaintvanne

  committed
  4833be6

• modify name

  

  jsaintvanne

  committed
  093bb79

• modify name

  

  jsaintvanne

  committed
  56907c1

• update tests

  

  jsaintvanne

  committed
  68f86d6

• change name

  

  jsaintvanne

  committed
  5ecb9c0

• update tests

  

  jsaintvanne

  committed
  18b2e4c

• adjust

  

  jsaintvanne

  committed
  afe107b

• some changes

  

  jsaintvanne

  committed
  b258f4f

• try update tests

  

  jsaintvanne

  committed
  50df3ca

• delete log files

  

  jsaintvanne

  committed
  4b1594b

Commits on Jun 5, 2019

• try pictures

  

  jsaintvanne

  committed
  87d62d8

• try gs test

  

  jsaintvanne

  committed
  cd82b5e

• update shebang, tests plot

  

  jsaintvanne

  committed
  05e48b7

Commits on Jun 12, 2019

• add gs in xml

  

  jsaintvanne

  committed
  8f07cf5

• delete gs in travis

  

  jsaintvanne

  committed
  34fac2c

• Merge pull request #29 from jsaintvanne/fix_zip

  Show description for 2b91cbe
  lecorguille

  authored
  2b91cbe

• change owner metams_rungc

  

  jsaintvanne

  committed
  108f461

• change owner shed

  

  jsaintvanne

  committed
  0c2cdfe

Commits on Jun 13, 2019

• some readme

  

  jsaintvanne

  committed
  0cc0982

• change id

  

  jsaintvanne

  committed
  5b00108

• just a change

  

  jsaintvanne

  committed
  245d14f

Commits on Jun 14, 2019

• change names

  

  jsaintvanne

  committed
  40fcf1f

• Merge pull request #32 from jsaintvanne/fix_zip

  Show description for 174a171
  lecorguille

  authored
  174a171

Commits on Jul 16, 2019

• add warning for cdf issue

  

  jsaintvanne

  committed
  11bb57e

Commits on Jul 17, 2019

• Correction for TIC and BPC from cdf files

  

  jsaintvanne

  committed
  65f2b20

Commits on Aug 12, 2019

• corection when 1 file

  

  jsaintvanne

  committed
  9f02a93

Commits on Aug 13, 2019

• some changes

  

  jsaintvanne

  committed
  927355b

Commits on Aug 20, 2019

• change data test

  

  jsaintvanne

  committed
  bbeef8c

Commits on Aug 21, 2019

• change

  

  jsaintvanne

  committed
  941411e

• change data test after change DB a little

  

  jsaintvanne

  committed
  7eb2b73

• add to delete

  

  jsaintvanne

  committed
  02696ce

• wrong branch

  

  jsaintvanne

  committed
  96beb44

• wrong branch

  

  jsaintvanne

  committed
  59db499

• correction changes

  

  jsaintvanne

  committed
  82c92db

• update data tests

  

  jsaintvanne

  committed
  942e68a

• update tests

  

  jsaintvanne

  committed
  b342e9e

Commits on Sep 2, 2019

• Merge pull request #35 from jsaintvanne/correct1file

  Show description for a7a6b82
  lecorguille

  authored
  a7a6b82

Commits on Sep 3, 2019

• Merge branch 'dev' into dev

  jsaintvanne

  authored
  2092ad3

• unpdate BPC

  jsaintvanne

  authored
  37843bc

• Merge pull request #38 from jsaintvanne/dev

  Show description for b301f1d
  lecorguille

  authored
  b301f1d

• add warning for CDF and result null correction

  

  jsaintvanne

  committed
  3bd7cb8

• delete correct null result

  

  jsaintvanne

  committed
  c7a5186

Commits on Sep 5, 2019

• Merge pull request #41 from jsaintvanne/dev

  Show description for c47a014
  lecorguille

  authored
  c47a014

Commits on Nov 5, 2019

• change pictures

  

  jsaintvanne

  committed
  9a8ce51

Commits on Jan 27, 2020

• delete fwhm

  jsaintvanne

  authored
  2efb673

• delete fwhm param

  jsaintvanne

  authored
  e45407a

• Merge pull request #43 from jsaintvanne/dev

  Show description for a89b822
  jsaintvanne

  authored
  a89b822

Commits on Apr 28, 2020

• change metams version

  

  jsaintvanne

  committed
  d7053e6

• change rbatch version

  

  jsaintvanne

  committed
  f244104

Commits on Apr 29, 2020

• versionning with macro

  

  jsaintvanne

  committed
  006bb51

• corrections for versionning

  

  jsaintvanne

  committed
  8235214

Commits on Apr 30, 2020

• correction of double space in DB

  

  jsaintvanne

  committed
  a03f793

• move authors and citations as macros

  

  jsaintvanne

  committed
  cb9c6a3

• change authors and citations with macro

  

  jsaintvanne

  committed
  df5fc6d

• correction of double spaces again

  

  jsaintvanne

  committed
  26fde20

Commits on May 6, 2020

• update runGC test data

  

  jsaintvanne

  committed
  59950a3

• update macro authors for planemo lint

  

  jsaintvanne

  committed
  67453d7

• put TODO in an isue

  

  jsaintvanne

  committed
  eb45457

• Merge pull request #45 from jsaintvanne/dev

  Show description for 1b3cc6c
  lecorguille

  authored
  1b3cc6c

Commits on Jun 18, 2020

• Full remove of fwhmparam not needed anymore

  yguitton

  committed
  74ecf53

Commits on Jun 26, 2020

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

  Show description for b3def33
  yguitton

  authored
  b3def33

Commits on Jul 2, 2020

• tool version update

  yguitton

  authored
  88163f9

Commits on Jul 15, 2020

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

  yguitton

  authored
  0030bc9

• change Travis branch target to dev

  yguitton

  authored
  da591ff

Commits on Feb 13, 2022

• Update version

  gallardoalba

  committed
  5f41ab4

Commits on Feb 14, 2022

• Merge pull request #50 from gallardoalba/Update_metaMS_version

  Show description for 0f4e17c
  yguitton

  authored
  0f4e17c

Commits on Oct 6, 2024

• Prep migration

  lecorguille

  committed
  4444c59

• Merge remote-tracking branch 'metams/prep_migration'

  lecorguille

  committed
  8a10f2a

Commits on Oct 8, 2024

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

  jsaintvanne

  committed
  7d9c621

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

  jsaintvanne

  committed
  b9aeb59

• change version name

  jsaintvanne

  committed
  e9a0367

• change version name test 2

  jsaintvanne

  committed
  fd571f0

• correct test of plot tool with expect_num_outputs

  jsaintvanne

  committed
  65568c2

Commits on Oct 9, 2024

• mv metams in tools folder

  lecorguille

  committed
  d3b6bd2

Commits on Oct 23, 2024

• Try to correct the indentation problem with lintr

  DamienCode404

  committed
  217570f

• Lintr error corrections

  DamienCode404

  committed
  0f42d95

• Lintr : Commented code should be removed.

  DamienCode404

  committed
  bc6be48

Commits on Nov 8, 2024

• fix: Test input file cannot be found.

  Show description for ae422d3
  DamienCode404

  committed
  ae422d3

• refactor: Change of structure for metams tool

  DamienCode404

  committed
  7d8000d

Commits on Nov 13, 2024

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

  DamienCode404

  committed
  6c7f5fe

Commits on Nov 14, 2024

• Fix: Rename file with lower-case character

  DamienCode404

  committed
  c2ba93e

• fix: Tool version with PEP 440

  DamienCode404

  committed
  aa882ad

• fix: Tool versioning

  DamienCode404

  committed
  c284f8f

• test-data: rungc

  DamienCode404

  committed
  769e93d

• test-data: metams_plot

  DamienCode404

  committed
  5274459

• fix: try with no single string in command rscript

  DamienCode404

  committed
  16ec8dd

• fix: change name file

  DamienCode404

  committed
  b56771e