v5.1.0+galaxy0 [2026-01]

This version refers to FROGS_5.1.0 suit.

Tools updated:

28 galaxy wrappers have been restructured in 4 tools to facilitate maintenance and future updates.

• FROGS Core 1-Main includes tools for : read processing (3 tools), removing chimera, ASV filtering, taxonomic affiliation, phylogenetic tree construction and ITS detection.
• FROGS Core 2-Clustering includes tools for : read demultiplexing, affiliation filtering and postprocessing, biom to tsv or tsv to biom conversion, and ASV and affilitation description.
• FROGS Func includes tools for : placing ASV sequences, predicting ASV and functions copy numbers, computing functions and pathways abundance tables.
• FROGS Stat includes tools for : importing data, calculating alpha and beta diversities, composition visulisation, sample ordination and clustering, manova analysis, and DESeq2 preprocess and visualisation.

These tools use the same reference databases and associated .loc files.

v4.2.0+galaxy1 [2025-05]

This version refers to FROGS_4.2.0 suit.

Bug corrected

Correction of a command syntaxe error in multiple tools :
preprocess.xml
remove_chimera.xml
normalisation.xml
frogsfunc_pathways.xml
frogsfunc_placeseqs.xml
phyloseq_alpha_diversity.xml
phyloseq_beta_diversity.xml
phyloseq_clustering.xml
phyloseq_composition.xml
phyloseq_import_data.xml
phyloseq_manova.xml
phyloseq_structure.xml

v4.2.0+galaxy0 [2025-04]

This version refers to FROGS_4.2.0 suit.

Function added:

• FROGSPreprocess : Allow vsearch to deal with AVITI reads (higher max quality value allowed)

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