v4.1.0+galaxy1 [2023-05]

v4.1.0+galaxy1

This version refers to FROGS_4.1.0 suit.

Function added:

• Preprocess : can deal with longreads sequencing

v4.0.1+galaxy1 [2022-06]

Bug corrected:

• Clustering : change output format for swarm_composition file from .tsv to .txt

v3.2.3+galaxy2

v3.2.3+galaxy2 [2021-06]

This version still refers to FROGS_3.2.3 suit.

Modifications:

with help of @lecorguille

• clean up xml code by using single quote, or python code following pep8 recommandations

• init macros for version, requirement, logo and help

• setup github actions for automatic galaxy testing

• precise XML test sections

• FROGS datamanager have been uploaded independently on the toolshed : https://toolshed.g2.bx.psu.edu/view/frogs/data_manager_frogs
  See README to remove previous installation of the datamanager without loosing previous reference databases downloaded.

v3.2.3.1

v3.2.3.1 [2021-06]

This version still refers to FROGS_3.2.3 suit.

Modifications:

• DESeq2 visualisation : correctly use the reference modality (in the tool conf pannel) as the expected modality2 in the deseq2_visualisation.py command line. Results were correct in the previous version but the reference condition was not the one precised by the user.

v3.2.3

v3.2.3 [2021-06]

Modifications:

• Affiliation_OTU : add a taxonomic rank parameter to correctly take into account taxonomy not defined on commonly used 7 ranks.
• Update R and package dependencies to version 4.0.5 (because of trouble installing DESeq2 version 1.26).
• Rename OTU FIlter and Affiliation Filter output files.

v3.2.2

v3.2.2 [2021-04]

Tools added:

• DESeq2 preprocess : Compute differential abundancy analysis
• DESeq2 visualisation : Create table and plots to explore and illustrate the differential abundant OTUs
• Filters has been splitted into to new tools : FROGS OTU Filters and FROGS Affiliations Filters.
  • FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did. For contamination research, user may now use a personnal multifasta contaminant reference.
  • FROGS Affiliation Filters delete OTU or mask affiliation that do not respect affiliation metrics criteria, or affiliated to undesirable (partial) taxon.
• FROGS datamanager is now available to manage affiliation reference database (frogs_db.loc for affiliation_OTU tool) thanks to @davidchristiany.

Contaminant database added

• add Arabidopsis thaliana chroloroplast sequence

Modifications:

• ITSx : add organism model option scanning, change default behavior regarding the trimming of conserved regions

• Use english typo for normalise and visualise

• rename phix_db.loc in contaminant_db.loc

• update tool dependencies version

v3.1.0

v3.1 [2018-02-12]

This release corresponds to the FROGS 3.1.0 release.

• Tools added:

  • ITSx : tool available for selecting and trimming ITS sequences based on ITSx tool
  • Affiliation Postprocess : resolve ambiguities due to inclusiv ITS, and aggregated OTU based on
    taxonomic affiliations

• Modifications:

  • use tool data table instead of simple loc files for filters, affiliation_OTU and affiliation_postprocess
  • Tree do no longer support Pynast alignment thanks to a template file