| This is FROGS version 3.1.0 Galaxy Wrappers FROGS: Find Rapidly OTUs through Galaxy Solution FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data. Authors: Valentin Marcon (valentin.marcon[a]inra.fr) Olivier Inizan (olivier.inizan[a]inra.fr) Laure Quintric (laure.quintric[a]ifremer.fr) Patrick Durand (pgdurand[a]ifremer.fr) Maria Bernard (maria.bernard[a]inra.fr) Géraldine Pascal (geraldine.pascal[a]inra.fr) 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_3_1_0
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| with bar plot and composition plot | 3.1 | 16.01 | |
| Converts a FROGS BIOM in fully compatible BIOM. | 3.1 | 16.01 | |
| Filters OTUs on several criteria. | 3.1 | 16.01 | |
| distance matrix | 3.1 | 16.01 | |
| merging, denoising and dereplication. | 3.1 | 16.01 | |
| with richness plot | 3.1 | 16.01 | |
| from 3 files: biomfile, samplefile, treefile | 3.1 | 16.01 | |
| Converts a TSV file in a BIOM file. | 3.1 | 16.01 | |
| Single-linkage clustering on sequences | 3.1 | 16.01 | |
| of samples using different linkage methods | 3.1 | 16.01 | |
| Taxonomic affiliation of each OTU's seed by RDPtools and BLAST | 3.1 | 16.01 | |
| Attribute reads to samples in function of inner barcode. | 3.1 | 16.01 | |
| with heatmap plot and ordination plot | 3.1 | 16.01 | |
| Process some metrics on clusters. | 3.1 | 16.01 | |
| Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics | 3.1 | 16.01 | |
| Process some metrics on taxonomies. | 3.1 | 16.01 | |
| Converts a BIOM file in TSV file. | 3.1 | 16.01 | |
| Reconstruction of phylogenetic tree | 3.1 | 16.01 | |
| Normalize OTUs abundance. | 3.1 | 16.01 | |
| perform Multivariate Analysis of Variance (MANOVA) | 3.1 | 16.01 | |
| Remove PCR chimera in each sample. | 3.1 | 16.01 | |
| Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. | 3.1 | 16.01 | |