| This is FROGS Galaxy Wrappers FROGS is a workflow designed to produce an ASV count matrix from high depth sequencing amplicon data. Adviced : reorder integrated_tool_panel.xml as indicated here : https://github.com/geraldinepascal/FROGS-wrappers#simplest-way |
hg clone https://toolshed.g2.bx.psu.edu/repos/frogs/frogs
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| perform Multivariate Analysis of Variance (MANOVA) | 4.1.0+galaxy3 | 20.05 | |
| with heatmap plot and ordination plot | 4.1.0+galaxy3 | 20.05 | |
| Attribute reads to samples in function of inner barcode | 4.1.0+galaxy3 | 20.05 | |
| Normalise ASV abundance. | 4.1.0+galaxy3 | 16.01 | |
| Remove PCR chimera in each sample | 4.1.0+galaxy3 | 20.05 | |
| with bar plot and composition plot | 4.1.0+galaxy3 | 20.05 | |
| Converts a TSV file in a BIOM file 1 | 4.1.0+galaxy3 | 20.05 | |
| from 3 files: biomfile, samplefile, treefile | 4.1.0+galaxy3 | 20.05 | |
| Taxonomic affiliation of each ASV's seed by RDPtools and BLAST | 4.1.0+galaxy3 | 20.05 | |
| Converts a BIOM file in TSV file | 4.1.0+galaxy3 | 20.05 | |
| distance matrix | 4.1.0+galaxy3 | 20.05 | |
| to extract and visualise differentially abundant ASVs or functions | 4.1.0+galaxy3 | 20.05 | |
| Extract the highly variable ITS1 and ITS2 subregions from ITS sequences | 4.1.0+galaxy3 | 20.05 | |
| Calculates functions abundances in each sample. | 4.1.0+galaxy3 | 16.01 | |
| merging, denoising and dereplication | 4.1.0+galaxy3 | 20.05 | |
| import a Phyloseq object and prepare it for DESeq2 differential abundance analysis | 4.1.0+galaxy3 | 20.05 | |
| with richness plot | 4.1.0+galaxy3 | 20.05 | |
| Places ASVs into a reference phylogenetic tree. | 4.1.0+galaxy3 | 16.01 | |
| Process some metrics on clusters | 4.1.0+galaxy3 | 20.05 | |
| Calculates pathway abundances in each sample. | 4.1.0+galaxy3 | 16.01 | |
| Process some metrics on taxonomies | 4.1.0+galaxy3 | 20.05 | |
| Filters clusters on several criteria. | 4.1.0+galaxy3 | 16.01 | |
| Filters ASVs on several affiliation criteria | 4.1.0+galaxy3 | 20.05 | |
| Single-linkage clustering on sequences | 4.1.0+galaxy3 | 20.05 | |
| of samples using different linkage methods | 4.1.0+galaxy3 | 20.05 | |
| Reconstruction of phylogenetic tree | 4.1.0+galaxy3 | 20.05 | |
| Converts a FROGS BIOM in fully compatible BIOM | 4.1.0+galaxy3 | 20.05 | |
| Aggregates ASVs based on alignment metrics | 4.1.0+galaxy3 | 20.05 | |