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comparison CHANGELOG.md @ 14:56b924f62165 draft

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"Update tests files for Galaxy tool wrapper"
author althonos
date Tue, 05 Apr 2022 23:18:49 +0000
parents fde43648cba0
children 64528877558f
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13:fde43648cba0 14:56b924f62165
3 3
4 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) 4 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
5 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). 5 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
6 6
7 ## [Unreleased] 7 ## [Unreleased]
8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha4...master 8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1...master
9
10 ## [v0.9.1] - 2022-04-05
11 [v0.9.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha4...v0.9.1
12
13 ### Changed
14 - Make the `genes.tsv` and `features.tsv` table contain all genes even when they come from a contig too short to be processed by the CRF sliding window.
15 - Replaced the `--force-clusters-tsv` flag with a `--force-tsv` flag to force writing TSV tables even when no genes or clusters were found in `gecco run` or `gecco annotate`.
9 16
10 ## [v0.9.1-alpha4] - 2022-03-31 17 ## [v0.9.1-alpha4] - 2022-03-31
11 [v0.9.1-alpha4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4 18 [v0.9.1-alpha4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4
12 19
13 Retrain internal model with: 20 Retrain internal model with:
14 ``` 21 ```
15 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \ 22 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \
16 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \ 23 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
17 -c mibig-2.0.proG2.clusters.tsv \ 24 -c mibig-2.0.proG2.clusters.tsv \
18 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.gff \ 25 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \
19 -o models/v0.9.1-alpha4 26 -o models/v0.9.1-alpha4
20 ``` 27 ```
21 28
22 ## [v0.9.1-alpha3] - 2022-03-23 29 ## [v0.9.1-alpha3] - 2022-03-23
23 [v0.9.1-alpha3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3 30 [v0.9.1-alpha3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3