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Repository qiime2_wrappers
Synopsis: 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.
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.
Type: unrestricted
Revision: 0:51b9b6b57732
This revision can be installed: True
Times cloned / installed: 231

Contents of this repository

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

Categories
Metagenomics - Tools enabling the study of metagenomes