| These wrappers were developed by Florian Begusch as part of his internship at Medical University of Graz, Center for Medical Research. (https://zmf.medunigraz.at/, https://zmf.medunigraz.at/en/core-facilities/cf-computational-bioanalytics/)
He would like to give his thanks 1) to Marija Durdevic for support on wrapper development and testing. 2) to Slave Trajanoski, who explained general metagenomics terminology and Galaxy (https://usegalaxy.org/). 3) to Alexander Mahnert, who provided data and was a key figure while testing some of the more exotic qiime commands. |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| - Taxonomy-based feature sequence filter. | 2018.4 | 16.01 | |
| - Collapse features by their taxonomy at the specified level | 2018.4 | 16.01 | |
| - De novo chimera filtering with vsearch. | 2018.4 | 16.01 | |
| - Summarize counts per sample. | 2018.4 | 16.01 | |
| - Create a distance matrix from a numeric Metadata column | 2018.4 | 16.01 | |
| - Compare query (observed) vs. reference (expected) sequences. | 2018.4 | 16.01 | |
| - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. | 2018.4 | 16.01 | |
| - Find and remove adapters in demultiplexed paired-end sequences. | 2018.4 | 16.01 | |
| - View sequence associated with each feature | 2018.4 | 16.01 | |
| - Apply the Mantel test to two distance matrices | 2018.4 | 16.01 | |
| - Closed-reference clustering of features. | 2018.4 | 16.01 | |
| - Rarefy table | 2018.4 | 16.01 | |
| - Convert to relative frequencies | 2018.4 | 16.01 | |
| - bioenv | 2018.4 | 16.01 | |
| - Beta diversity (phylogenetic) | 2018.4 | 16.01 | |
| - Beta diversity rarefaction | 2018.4 | 16.01 | |
| - Interactively explore Metadata in an HTML table | 2018.4 | 16.01 | |
| - Add pseudocount to table | 2018.2 | 16.01 | |
| - Volatility analysis | 2018.4 | 16.01 | |
| - Hierarchical clustering using feature correlation. | 2018.4 | 16.01 | |
| - Alpha diversity (phylogenetic) | 2018.4 | 16.01 | |
| - Alpha diversity correlation | 2018.4 | 16.01 | |
| - Combine collections of feature taxonomies | 2018.4 | 16.01 | |
| - Group samples or features by a metadata column | 2018.4 | 16.01 | |
| - Export data from a QIIME 2 Artifact or Visualization. | 2018.4 | 16.01 | |
| - Quality filter based on joined sequence quality scores. | 2018.4 | 16.01 | |
| - Apply ANCOM to identify features that differ in abundance. | 2018.4 | 16.01 | |
| - Midpoint root an unrooted phylogenetic tree. | 2018.4 | 16.01 | |
| - Subsample table | 2018.4 | 16.01 | |
| - Linear mixed effects modeling | 2018.4 | 16.01 | |
| - Export data from a QIIME 2 Artifact or Visualization. | 2018.4 | 16.01 | |
| - Remove features from table if they're not present in tree. | 2018.4 | 16.01 | |
| - Balance Summary | 2018.4 | 16.01 | |
| - Alpha diversity | 2018.4 | 16.01 | |
| - Combine multiple tables | 2018.4 | 16.01 | |
| - Compute first distances or distance from baseline between sequential states | 2018.4 | 16.01 | |
| - Add pseudocount to table | 2018.4 | 16.01 | |
| - Principal Coordinate Analysis | 2018.4 | 16.01 | |
| - Beta diversity (phylogenetic) - High Performance Computation | 2018.4 | 16.01 | |
| - Core diversity metrics (phylogenetic and non- phylogenetic) | 2018.4 | 16.01 | |
| - Denoise and dereplicate single-end sequences | 2018.4 | 16.01 | |
| - Visualize and Interact with Principal Coordinates Analysis Plots | 2018.4 | 16.01 | |
| - Compute first differences or difference from baseline between sequential states | 2018.4 | 16.01 | |
| - Alpha rarefaction curves | 2018.4 | 16.01 | |
| - Nonparametric microbial interdependence test | 2018.4 | 16.01 | |
| - Demultiplex paired-end sequence data generated with the EMP protocol. | 2018.4 | 16.01 | |
| - Simplicial Linear mixed effects regression | 2018.4 | 16.01 | |
| - Export data from a QIIME 2 Artifact or Visualization. | 2018.4 | 16.01 | |
| - Train the naive_bayes classifier | 2018.4 | 16.01 | |
| - Procrustes Analysis | 2018.4 | 16.01 | |
| - Find and remove adapters in demultiplexed single-end sequences. | 2018.4 | 16.01 | |
| - Extract reads from reference | 2018.4 | 16.01 | |
| - Dendrogram heatmap. | 2018.4 | 16.01 | |
| - Visualize Deblur stats per sample. | 2018.4 | 16.01 | |
| - Import data into a new QIIME 2 Artifact. | 2018.4 | 16.01 | |
| - Positional conservation and gap filtering. | 2018.4 | 16.01 | |
| - Paired pairwise distance testing and boxplots | 2018.4 | 16.01 | |
| - Visualize taxonomy with an interactive bar plot | 2018.4 | 16.01 | |
| - Dereplicate sequences. | 2018.4 | 16.01 | |
| - Merge features and taxonomy into a single biom file. | 2018.4 | 16.01 | |
| - Beta diversity | 2018.4 | 16.01 | |
| - Denoise and dereplicate single-end pyrosequences | 2018.4 | 16.01 | |
| - Demultiplex sequence data generated with the EMP protocol. | 2018.4 | 16.01 | |
| - Open-reference clustering of features. | 2018.4 | 16.01 | |
| - BLAST+ consensus taxonomy classifier | 2018.4 | 16.01 | |
| - Deblur sequences using a 16S positive filter. | 2018.4 | 16.01 | |
| - De novo multiple sequence alignment with MAFFT | 2018.4 | 16.01 | |
| - Filter samples from a distance matrix. | 2018.4 | 16.01 | |
| - Pre-fitted sklearn-based taxonomy classifier | 2018.4 | 16.01 | |
| - Supervised learning regressor. | 2018.4 | 16.01 | |
| - Beta diversity group significance | 2018.4 | 16.01 | |
| - Hierarchical clustering using gradient information. | 2018.4 | 16.01 | |
| - Construct a phylogenetic tree with FastTree. | 2018.4 | 16.01 | |
| - Isometric Log-ratio Transform | 2018.4 | 16.01 | |
| - Reference-based chimera filtering with vsearch. | 2018.4 | 16.01 | |
| - Simplicial Ordinary Least Squares Regression | 2018.4 | 16.01 | |
| - Supervised learning classifier. | 2018.4 | 16.01 | |
| - Exclude sequences by alignment | 2018.4 | 16.01 | |
| - Train an almost arbitrary scikit-learn classifier | 2018.4 | 16.01 | |
| - Convert to presence/absence | 2018.4 | 16.01 | |
| - Filter features from sequences | 2018.4 | 16.01 | |
| - VSEARCH consensus taxonomy classifier | 2018.4 | 16.01 | |
| - Quality filter based on sequence quality scores. | 2018.4 | 16.01 | |
| - Paired difference testing and boxplots | 2018.4 | 16.01 | |
| - Evaluate expected vs. observed taxonomic composition of samples | 2018.4 | 16.01 | |
| - Filter features from table | 2018.4 | 16.01 | |
| - Visualize and Interact with a procrustes plot | 2018.4 | 16.01 | |
| - Taxonomy-based feature table filter. | 2018.4 | 16.01 | |
| - Generate a heatmap representation of a feature table | 2018.4 | 16.01 | |
| - Summarize table | 2018.4 | 16.01 | |
| - De novo clustering of features. | 2018.4 | 16.01 | |
| - Alpha diversity comparisons | 2018.4 | 16.01 | |
| - Deblur sequences using a user-specified positive filter. | 2018.4 | 16.01 | |
| - Demultiplex single-end sequence data with barcodes in- sequence. | 2018.4 | 16.01 | |
| - Microbial maturity index prediction. | 2018.4 | 16.01 | |
| - Identify core features in table | 2018.4 | 16.01 | |
| - Filter samples from table | 2018.4 | 16.01 | |
| - Demultiplex paired-end sequence data with barcodes in- sequence. | 2018.4 | 16.01 | |
| - Combine collections of feature sequences | 2018.4 | 16.01 | |
| - Denoise and dereplicate paired-end sequences | 2018.4 | 16.01 | |
| - Core diversity metrics (non-phylogenetic) | 2018.4 | 16.01 | |
| - Join paired-end reads. | 2018.4 | 16.01 | |