# v3.2.1 [2021-02-22]

### Bug fixed
* correct reversecomp function by taking into account S and W IUPAC nucleotides

# v3.2 [2021-01-13]

### Tools added:
  * DESeq2 preprocess : Compute differential abundancy analysis
  * DESeq2 visualization : 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.

### Function added
  * Affiliation_postprocess : taxon-ignore option added, to ignore some taxon like "unknown species" during the aggreagation process. Multiple taxon may be provided as well as partial taxon, like "sp."
  * Preprocess : now accept input sequence file as Fasta format (format automatically detected) for already contiged input.
  * Affiliations_stat : check that the number of rank name correspond to the number of ranks in input biom file
  * FROGSSTAT Phyloseq import : check sample names consistency between sample metadata and input biom file
  * FROGS OTU Filters filters OTU on presence/absence, abundances and contamination as Filters did.


### Bug fixed
  * Affiliation_postprocess : correctly compare de %coverage and the coverage threshold.
  * FROGSSTAT Structure : plot_heatmap now take into account ordination method and dissimilarity matrix
  * addAffiliation2biom : do not split partial description from blast reference ID
  * tsv_2_biom now keep initial OTU order (Cluster_1 is the most abundant one and Cluster_X the less abundant one)

### Other improvements
  * All python scripts are now in python 3
  * FROGSSTAT Phyloseq and FROGSSTAT DESeq now generate notebook_html instead of classical HTML output file. This facilitates code maintenance.

# v3.1 [2018-01-08]

### Bug fixed
  * Tsv_to_Biom : manage quotes added by Excel
  * Affiliation_postprocess : bug when references are not in the troncated amplicon database.

### Modifications:
  * Tree do no longer support Pynast alignment thanks to a template file
  * XML wrappers, images and loc files are externalized to [FROGS-wrappers](https://github.com/geraldinepascal/FROGS-wrappers) (FROGS is now available on Toolshed and conda )

# v3.0.0 [2018-10-10]
### 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

### Functions added:
  * Preprocess : keep and filter non overlapped reads (particularly important for amplicon polymorphe in length)
  * Affiliation : non overlapped read generate FROGS_combined OTU that are affiliated thanks to Needl (http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html) global alignment

### Modifications:
  * General : Use GALAXY_SLOTS variable in XML. 
              Upadate version dependancies
              Remove redirection to /dev/null
              Update test/test.sh
              Update XML doc
              Update graphical charter of HTML outputs
              HTML reports now work on secured server by using of https instead of http to all JavaScript and CSS URLs (https://github.com/geraldinepascal/FROGS/issues/34).
  * Preprocess : add VSEARCH and PEAR (https://sco.h-its.org/exelixis/web/software/pear/ only for command line usage because of PEAR licence) options to merge reads
  * Clustering : deal with artificially combined reads
  * FROGSSTAT tools do not call anymore external script from urls. Additionnal library dependancies 
    added : https://github.com/mahendra-mariadassou/phyloseq-extended/releases
  * FROGSSTAT import : can take FROGS specific biom file
  * FROGS TSV_to_Biom : keeps original type of metadata (float, int or list instead of string)
                        remove quotes added by Excel when exporting abundance tsv file in text file

### Bugs fixes:
  * Phyloseq import: bug when Tree is None
  * libexec/derepSamples : bug with temporary files name

# v2.0.0  [2017-08-08]
### Tools added : 
  * Tree : perform phylogenetic tree reconstruction based on Mafft or Pynast follow by Fasttree and phangorn
  * FROGS Phyloseq Import Data : import data from 3 files: biomfile, samplefile, treefile into a phyloseq R object.
  * FROGS Phyloseq Composition Visualization with bar plot and composition plot
  * FROGS Phyloseq Alpha Diversity with richness plot
  * FROGS Phyloseq Beta Diversity distance matrix
  * FROGS Phyloseq Structure
  * FROGS Phyloseq Clustering
  * FROGS Phyloseq Manova 

### libexec program added:
  * rooted_tree.R : Rscript to root FastTree tree. (used by Tree)

### Bugs fixes:
  * Preprocess : min overlap at least equal to 1
  * biom2tsv : not working with stdBiom containing RDP affiliation, not working when emtpy metadata

### Functions added:
  * Preprocess: add Flash mismatch rate option

# v1.4.0  [2017-02-04]
### Bugs fixes:
  * Preprocess: error in final dereplication with hudge number of samples.
  * Remove_chimera: error when using library Queue and hudge number of samples.
  * Clusters_stat: error with empty samples in hierarchical clustering.
  * Filters: error when only the filter on contamination is used.
  * Filters: bug when using other filters than abundance (check parameter when None).
  * Tsv2Biom : bug fix when using a tsv file comming from a standard biom file
  * Affiliations_stat : bug in rarefaction step computation when sample are empty

### Functions added:
  * Preprocess: new amplicon length graph.
  * Clustering: reduce memory consumption and execution time for the step swarm2biom.
  * Affiliations_stat: more details in alignment heatmap.


# v1.3.0  [2016-04-18]
### Update notes:
This section contain actions to execute if you update a previous FROGS version to this version.

  * The directory lib has been created and librairies have been renamed. In installation step 2 if you have added `FROGS/bin` in the PYTHONPATH you can remove this path and add `FROGS/lib` instead.
  * The directory libexec has been created. In installation step 2 if you have added `FROGS/bin` in the PATH you can remove this path and add `FROGS/libexec` instead.
  * The tools are moved in app directory. If you use FROGS in galaxy you must change the tool_conf.xml:

        ...
        <section id="FROGS_wrappers" name="FROGS">
            <tool file="FROGS/app/upload_tar.xml" />
            <tool file="FROGS/app/demultiplex.xml" />
            <tool file="FROGS/app/preprocess.xml" />
            <tool file="FROGS/app/clustering.xml" />
            <tool file="FROGS/app/remove_chimera.xml" />  
            <tool file="FROGS/app/filters.xml" />
            <tool file="FROGS/app/affiliation_OTU.xml" />
            <tool file="FROGS/app/clusters_stat.xml" />
            <tool file="FROGS/app/affiliations_stat.xml" />
            <tool file="FROGS/app/biom_to_stdBiom.xml" />
            <tool file="FROGS/app/biom_to_tsv/biom_to_tsv.xml" />
            <tool file="FROGS/app/tsv_to_biom.xml" />
            <tool file="FROGS/app/normalisation.xml" />
        </section>
        ...

### Bugs fixes:
  * Preprocess: missing values in lengths distribution graph.


# v1.2.0  [2016-04-06]
### Update notes:
This section contain actions to execute if you update a previous FROGS version to this version.

  * The repository structure has been changed: tools have been moved in sub-directories. It is necessary to re-do the following installation steps: '6. Add tools in galaxy' and '7. Set memory and parallelisation settings'.
  * The tool FROGS\_tsv\_to\_biom has been added. It is necessary to add the following line in galaxy tool_conf.xml: `<tool file="FROGS/tools/tsv_to_biom/tsv_to_biom.xml" />`.

### Bugs fixes:
  * Too large number of temp files in clustering tool.
  * Fix bug with BIOM without observation metadata in filters.
  * Fix bug with heatmap hover in affiliations_stat.

### Functions added:
  * Add tool to convert a TSV file in BIOM file.
  * Default BIOM becomes mono-line.
  * Reduce the BIOM file size (identation 4 -> 2 in pretty_print).
  * Change the repository structure (one directory by tool).
  * Use biomTools in normalisation.
  * Number of sampled sequences becomes required in normalisation tool.
  * Add better wrapping for sample name fields in preprocess.
  * Add check on minimum amplicon size value in preprocess.
  * Add vsearch version in remove chimera log.
  * Add cutadapt version in preprocess log.


# v1.1.0  [2015-11-30]
### Bugs fixes:
  * Fix bug with empty blast_taxonomy in BIOM.
  * Fix bug with checkall in chrome.
  * Fix bug with CSV extraction in HTML outputs.
  * Fix bug 'Exception in thread QueueFeederThread' in slow systems.

### Functions added:
  * Add '% kept' in preprocess.
  * Add checks on samples names in preprocess.
  * Add DenseData management in BIOM.
  * Add the biom1 datatype in tools.


# v1.0.0  [2015-09-18]
  First package.
