| 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) | 3.2.2 | 16.01 | |
| with heatmap plot and ordination plot | 3.2.2 | 16.01 | |
| Attribute reads to samples in function of inner barcode. | 3.2.2 | 16.01 | |
| Normalise OTUs abundance. | 3.2.2 | 16.01 | |
| Remove PCR chimera in each sample. | 3.2.2 | 16.01 | |
| with bar plot and composition plot | 3.2.2 | 16.01 | |
| Converts a TSV file in a BIOM file. | 3.2.2 | 16.01 | |
| from 3 files: biomfile, samplefile, treefile | 3.2.2 | 16.01 | |
| Process some metrics on taxonomies. | 3.2.2 | 16.01 | |
| Converts a BIOM file in TSV file. | 3.2.2 | 16.01 | |
| distance matrix | 3.2.2 | 16.01 | |
| to extract and visualise differentially abundant OTUs | 3.2.2 | 16.01 | |
| Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. | 3.2.2 | 16.01 | |
| Taxonomic affiliation of each OTU's seed by RDPtools and BLAST | 3.2.2 | 16.01 | |
| merging, denoising and dereplication. | 3.2.2 | 16.01 | |
| import a Phyloseq object and prepare it for DESeq2 differential abundance analysis | 3.2.2 | 16.01 | |
| with richness plot | 3.2.2 | 16.01 | |
| Process some metrics on clusters. | 3.2.2 | 16.01 | |
| Filters OTUs on several criteria. | 3.2.2 | 16.01 | |
| Filters OTUs on several affiliation criteria. | 3.2.2 | 16.01 | |
| Single-linkage clustering on sequences | 3.2.2 | 16.01 | |
| of samples using different linkage methods | 3.2.2 | 16.01 | |
| Reconstruction of phylogenetic tree | 3.2.2 | 16.01 | |
| Converts a FROGS BIOM in fully compatible BIOM. | 3.2.2 | 16.01 | |
| Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics | 3.2.2 | 16.01 | |
| 3.2.2 | 16.01 | ||
| Name | Version | Data Tables |
|---|---|---|
| frogs_data_manager | 0.0.1 | frogs_db |