Workflow: Functional analyis of sequences that match the 16S SSU
Fetched 2024-09-08 14:46:34 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| 16S_matches | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| prune_tree |
../tools/qiime-filter_tree.cwl
(CommandLineTool)
|
||
| krona_setup |
../tools/krona_setup.cwl
(CommandLineTool)
|
||
| extract_observations |
../tools/extract_observations.cwl
(CommandLineTool)
|
||
| visualize_otu_counts |
../tools/krona.cwl
(CommandLineTool)
|
visualize using krona | |
| modify_taxonomy_table |
../tools/modify_taxonomy_table.cwl
(CommandLineTool)
|
generate a modified tsv taxonomy file that works with the current web app | |
| create_otu_text_summary |
../tools/biom-summarize_table.cwl
(CommandLineTool)
|
||
| update_krona_chart_urls |
../tools/update_krona_chart_urls.cwl
(CommandLineTool)
|
||
| convert_otu_counts_to_hdf5 |
../tools/biom-convert.cwl
(CommandLineTool)
|
||
| pick_closed_reference_otus |
../tools/qiime-pick_closed_reference_otus.cwl
(CommandLineTool)
|
||
| convert_new_biom_to_classic |
../tools/biom-convert.cwl
(CommandLineTool)
|
||
| convert_new_biom_to_old_biom |
../tools/biom-convert.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| tree | File | ||
| biom_tsv | File | ||
| biom_hdf5 | File | ||
| biom_json | File | ||
| krona_input | File | ||
| kingdom_counts | File | ||
| otu_table_summary | File | ||
| otu_visualization | File | ||
| qiime_assigned_taxonomy | File | ||
| qiime_sequences-filtered_otus | File | ||
| qiime_sequences-filtered_clusters | File |
Permalink:
https://w3id.org/cwl/view/git/71d9c83761ea301a895dd669902979ef5a4b279b/workflows/16S_taxonomic_analysis.cwl
