Releases: RECETOX/galaxytools
Releases · RECETOX/galaxytools
v0.6.3
What's Changed
- Update DOI badge and remove old Matrix badge by @hechth in #731
- Add .zenodo.json for automated Zenodo archive updates by @Copilot in #733
Full Changelog: v0.6.2...v0.6.3
Contributors
hechth
Assets 2
v0.6.2
v0.6.1
What's Changed
- first draft by @ChangLiuuczlcl8 in #474
- Skyline transition list generation tool. by @hechth in #607
- galaxy wrapper for the scp tool by @KristinaGomoryova in #625
- Added first set of bioconductor-msnbase tools by @hechth in #627
- Adding new generation of table manipulation tools by @hechth in #610
- PR for the recetox-boxplot tool by @KristinaGomoryova in #631
- Replaced output of biotransformer from tsv to tabular by @acquayefrank in #641
- Update planemo CI pipeline by @hechth in #649
- Fixed issue in QCxMS by @hechth in #647
- Updated license specification. by @hechth in #656
- ms target screen: improve documentation and added different input data types by @hechth in #655
- Replaced output of matchms from tsv to tabular by @acquayefrank in #644
- Bug fix - Isolib issue 651 by @acquayefrank in #658
- ipaPy2 PR by @acquayefrank in #629
- wavica: accept tabular as input by @hechth in #659
- updated documentation and improved output file labeling by @hechth in #660
- updated MSMetaenhancer version as well as output by @acquayefrank in #671
- Created new tool request issue template by @hechth in #674
- Fix for issue number 651 - isolib: output is invalid if using 10% intensity cut-off by @acquayefrank in #673
- Added version update issue template by @hechth in #678
- Updated spec2vec similarity tool by @hechth in #686
- Added rdata.xcms.group to RAMclustR datatypes and updated RAMClustR to 1.3.1 by @hechth in #679
- Implement wrapper for bioconductor-mzR convert by @hechth in #688
- Added mzspeclib convert & describe tools by @hechth in #682
- Updated matchms suite to 0.30.2 by @hechth in #690
- Added functionality for parsing extra columns when using isolib by @acquayefrank in #692
- Fixes #602 - waveica: accept tables with additional columns by @acquayefrank in #687
- mztab-m validation tool by @hechth in #693
- added wtv to galaxy tools by @acquayefrank in #676
- Added tool to query frequence of SAPs for preotins using UniProt and DbSNP by @hechth in #695
- matchms convert: don't remove ionmode by @hechth in #699
- Fixed failing linters and tests by @hechth in #697
- fix linting for bioconductor-msnbase tools by @hechth in #704
- fix linting for bioconductor-scp tool by @hechth in #706
- Enh/666 change output label by @acquayefrank in #701
- fix rcx_boxplot lint errors by @hechth in #711
- fix table tools lint errors by @hechth in #713
- Update spec2vec from 0.8.0 to 0.9.1 by @Copilot in #719
- for images prefer cerit-hosted singularity by @martenson in #715
- updated workflow version to galaxy release 25.1 by @hechth in #726
- AOP-toolkit (aoptk) initiation, wrappers for Chemical-Identifier/Publication-Tracker by @rdurnik in #724
New Contributors
- @ChangLiuuczlcl8 made their first contribution in #474
- @acquayefrank made their first contribution in #641
- @Copilot made their first contribution in #719
- @rdurnik made their first contribution in #724
Full Changelog: v0.5.0...v0.6.1
Contributors
martenson, acquayefrank, and 4 other contributors
Assets 2
v0.5.0
What's Changed
- recetox-aplcms version 0.13.2 by @hechth in #562
- Initial commit of the rcx-tk galaxy wrapper by @KristinaGomoryova in #563
- Added group value for standard by @zargham-ahmad in #566
- Mfassignr ISOFiltr tool by @hechth in #565
- Galaxy wrappers for the MFAssignR functions by @KristinaGomoryova in #567
- Update ci.yaml by @hechth in #569
- fixed biotransformer tests by @hechth in #570
- Fixed cut and mass parameters in mfassignr_snplot tool by @hechth in #573
- planemo test biocontainers for all subdirectories by @KristinaGomoryova in #574
- Added ms2deepscore tool suite by @zargham-ahmad in #568
- Galaxy wrapper for MFAssignR::FindRecalSeries tool by @KristinaGomoryova in #581
- hotfix for findrecalseries by @hechth in #582
- Updated recetox-aplcms to 0.13.3 by @hechth in #584
- added target screening tool by @hechth in #587
- Add tstep and etemp parameters to the QCxMS tool by @wverastegui in #586
- signal-to-noise separated into ratio and noise in IsoFiltR by @KristinaGomoryova in #594
- Force input of rt correction in recetox-aplcms to be a collection by @hechth in #596
- More parameters added to MFAssignR: MFAssignCHO and MFAssign function by @KristinaGomoryova in #595
- Revert "Force input of rt correction in recetox-aplcms to be a collection" by @hechth in #601
- rcx-aplcms version 0.13.4 by @hechth in #605
- Updated mfassignr to version 1.1.2 by @hechth in #606
- isolib: added option to export to tabular by @hechth in #599
New Contributors
- @KristinaGomoryova made their first contribution in #563
Full Changelog: v0.4.0...v0.5.0
Contributors
hechth, KristinaGomoryova, and 2 other contributors
Assets 2
v0.4.0
What's Changed
- Update to matchms 0.20.X and include Spec2Vec similarity score by @maximskorik in #321
- recetox-aplcms: update to 0.12.0 by @xtrojak in #390
- Include test-data in .shed.yml for riassigner and recetox_xmsannotator by @cat-bro in #391
- Update matchms to 0.22.0 by @hechth in #395
- updated CI and PR github actions from IUC by @hechth in #400
- updated PAT by @hechth in #401
- matchms: added filters and test and fixed linter warnings by @zargham-ahmad in #402
- Added matchms add key tool by @zargham-ahmad in #404
- Improved formatter.py performance by @zargham-ahmad in #403
- matchms convert: add MS-LIMA MSP style by @zargham-ahmad in #408
- Molecular optimization tool by @wverastegui in #394
- deployment CI fix by @zargham-ahmad in #410
- add dummy tests for aplcms by @hechth in #411
- bumped galaxy version in all wrapers to trigger toolshed update by @hechth in #413
- Update matchms to 0.23.1 by @hechth in #416
- Add EDAM identifiers: Retip and recetox-msfinder by @zargham-ahmad in #420
- Update matchms molecular networking tool by @hechth in #436
- Updated matchms version to 0.24.0 by @zargham-ahmad in #442
- Added tool: matchms_subsetting_tool by @zargham-ahmad in #437
- fix matchms outputs to existing types by @bernt-matthias in #438
- Added tool: matchms_metadata_merge by @zargham-ahmad in #428
- updated python in matchms merge and subsetting tool by @zargham-ahmad in #446
- Removes coordination complexes compounds by @wverastegui in #441
- Updated recetox-msfinder output and version by @zargham-ahmad in #451
- Update matchms_formatter.xml with OPENBLAS_NUM_THREADS=1 by @hechth in #452
- try more threads by @hechth in #453
- try adding RLIMIT_NPROC and removed explicit pandas dependency by @hechth in #455
- re-added pandas dependency by @hechth in #456
- Implemented
matchms remove keytool by @hechth in #460 - matchms_filtering: Added derive_precursor_mz_from_parent_mass filter by @zargham-ahmad in #475
- Updated matchms filtering tool to use matchms function by @zargham-ahmad in #478
- Updated recetox_msfinder to v3.5.2-rcx2 by @zargham-ahmad in #483
- Disabled key conversion in matchms tools by @zargham-ahmad in #484
- Qcxms by @zargham-ahmad in #421
- Read RI from comments and add them to RI column field by @wverastegui in #486
- High-res peak overwriting with theoretical MS tool by @wverastegui in #487
- matchms metadata match: added formula to "equal_match" options by @zargham-ahmad in #489
- fix use_theoretical_mz_annotations tools by @hechth in #492
- next attempt by @hechth in #493
- Update qcxms_prod_run.xml by @hechth in #494
- QCxMS New Version by @zargham-ahmad in #497
- matchms add key, matchms remove key: Added multiple keys handling by @zargham-ahmad in #502
- MeOX & TMS GC-Derivatization Tool by @wverastegui in #503
- CI update by @hechth in #506
- Change output csv types to tsv by @zargham-ahmad in #504
- Updated MSMetaEnhancer to 0.4.0 by @zargham-ahmad in #512
- Fixed GFN1-xTB selection issue in qcxms_neutral_run tool by @zargham-ahmad in #513
- Updated RAMClustR tool by @zargham-ahmad in #514
- matchms scores formatter: added key parameter by @zargham-ahmad in #520
- Isolib tool first version by @hechth in #521
- Update isolib.xml by @hechth in #522
- isolib: fix rt column reading and writing by @hechth in #525
- Updated riassigner to 0.4.1 by @zargham-ahmad in #532
- Update WaveICA to outputs by @zargham-ahmad in #533
- Updated WaveICA to allow integer class column type by @zargham-ahmad in #537
- Tool for GC annotation by @wverastegui in #536
- Fixed typos by @wverastegui in #538
- Updated RAMClustR to allow tsv for rectetox-aplcms inputs by @zargham-ahmad in #539
- RAMClustR: fixed sample name reading for tabular inputs by @zargham-ahmad in #541
- Update ci.yaml by @hechth in #543
- updated matchms to 0.25.0 by @hechth in #544
- Update matchms help.xml by @hechth in #546
- styling all R files in folder by @hechth in #548
- Implemented dedicated require filters matchms tool by @zargham-ahmad in #517
- Update msmetaenhancer.xml by @hechth in #550
- Updated matchms remove spectra tool by @hechth in #553
- WaveICA: Added boolean parameter to output feature table and metadata table separately by @zargham-ahmad in #555
- Expanded creator tag by @wverastegui in #556
- Added boolean to retain molecule name by @wverastegui in #557
- Updated matchms to 0.27.0 by @zargham-ahmad in #558
- EDAM annotations for QCxMS and xTB tools by @wverastegui in #560
New Contributors
- @cat-bro made their first contribution in #391
- @bernt-matthias made their first contribution in #438
Full Changelog: v0.3.0...v0.4.0
Contributors
hechth, xtrojak, and 5 other contributors
Assets 2
Release v0.3.0
What's Changed
- matchms: add tabular datatype explicitly by @martenson in #206
- RAMClustR tool form improvement by @xtrojak in #220
- Bump RIAssigner to 0.3.2 by @hechth in #222
- MSMetaEnhancer log as an optional output by @xtrojak in #223
- Update CI to use planemo action by @martenson in #228
- Implemented basic RI filtering via matchms by @hechth in #227
- enable upload to MTS by @martenson in #231
- Update MSME to v0.2.0 by @xtrojak in #241
- upload all repos with green light to MTS by @martenson in #236
- waveica: remove obsolete file from shed.yml by @martenson in #245
- update biotransformer to 3.0 by @martenson in #235
- detect errors in all tools by @martenson in #247
- add new tool: msp_split by @wverastegui in #234
- Update MSME version to v0.2.1 by @xtrojak in #252
- Update RAMClustR to version 1.2.4 by @xtrojak in #254
- MSME matchms logging level by @xtrojak in #259
- MSME v0.2.2 by @xtrojak in #262
- Tool to merge MSP files by @wverastegui in #263
- Update MSME to v0.2.3 by @xtrojak in #267
- Add apLCMS Two-Step Hybrid wrapper by @maximskorik in #264
- apLCMS split to steps by @xtrojak in #265
- apLCMS: input collections by @xtrojak in #269
- RAMClustR: Add define experiment wrapper to shed by @xtrojak in #280
- galaxytools: update Zenodo badge in README.md by @maximskorik in #287
- matchms similarity: Added NeutralLossesCosine metric by @zargham-ahmad in #281
- matchms similarity: fix bug in RI filtering by @maximskorik in #300
- Update MSMetaEnhancer to v0.2.4 by @xtrojak in #297
- RAMClustR: removed quotes in SpecAbundance output by @zargham-ahmad in #303
- Fixed similarity bug for RI filtering & fixed formatter bug by @hechth in #302
- WaveICA: Separate input and formats support by @zargham-ahmad in #304
- matchms: switch to
Scoresobjects by @maximskorik in #289 - matchms: add wrapper for matchMS networking subpackage by @maximskorik in #286
- Update MSMetaEnhancer to v0.2.5 by @xtrojak in #306
- Update version of actions in workflows by @xtrojak in #309
- Update MSME
v0.2.5versiongalaxy1by @xtrojak in #311 - msfinder wrapper by @zargham-ahmad in #313
- add wrapper for training Spec2Vec in Galaxy by @maximskorik in #314
- add mzml-validation tool by @maximskorik in #319
- Msfinder version update by @zargham-ahmad in #324
- recetox-aplcms
v0.10.1by @xtrojak in #317 - Update help.xml by @xtrojak in #325
- RIAssigner 0.3.4 by @hechth in #331
- Update recetox-aplcms to v0.10.3 by @xtrojak in #329
- Reworked msp_split tool by @hechth in #343
- Tool to convert mass spectral libraries by @hechth in #339
- Updated recetox_aplcms_align_features with cluster by @zargham-ahmad in #345
- MSMetaEnhancer: get rid of Fontconfig error by @xtrojak in #347
- MSMetaEnhancer 0.3.0 by @xtrojak in #352
- Polish RMassBank by @xtrojak in #351
- Add matchms tool for metadata extraction by @xtrojak in #356
- Add matchms_metadata_export to shed by @xtrojak in #357
- update to recetox-aplcms 0.11.0 by @hechth in #353
- Fixed bug in recetox-aplcms remove_noise by @hechth in #362
- Updated matchms_convert tool by @zargham-ahmad in #358
- Updated Labels in recetox_aplcms tools by @zargham-ahmad in #346
- Update utils.R to fix bug introduced in PR merge by @hechth in #363
- Bump biotransformer to version 3.0_20230403 by @xtrojak in #360
- Remove aplcms_to_ramclustr_converter by @xtrojak in #366
- RAMClustR: update to 1.3.0 by @zargham-ahmad in #364
- Create add_issue_to_project.yml by @hechth in #344
- Create project_automation.yaml by @hechth in #372
- Update slash.yaml by @hechth in #377
- Add EDAM identifiers to recetox-aplcms suite by @hechth in #375
- Add EDAM identifiers to ramclustr by @zargham-ahmad in #376
- MSMetaEnhancer: Add EDAM identifiers by @xtrojak in #379
- BioTransformer: fix tests by @xtrojak in #385
- RIAssigner: Add EDAM identifiers by @xtrojak in #381
- Updated waveica for new outputs from recetox-aplcms by @zargham-ahmad in #378
- BioTransformer: Add EDAM identifiers by @xtrojak in #382
- Cleanup xmsannotator wrappers by @xtrojak in #367
New Contributors
- @wverastegui made their first contribution in #234
- @zargham-ahmad made their first contribution in #281
Full Changelog: v0.2.0...v0.3.0
Contributors
martenson, hechth, and 4 other contributors
Assets 2
Release v0.2.0
Merge pull request #217 from xtrojak/ramclustr-define-experiment RAMClustR experimental design input
Initial release
Merge pull request #78 from martenson/update_ci bring CI fixes from upstream
Zenodo Release
Merge pull request #78 from martenson/update_ci bring CI fixes from upstream