Workflow: fasta2taxa-plot
Fetched 2023-01-12 01:35:45 GMT
Verified with cwltool version 3.1.20221201130942
Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| samples-fna | File | ||
| sample-mapping | File | ||
| min-observations-per-otu | Integer (Optional) | ||
| summarize-for-taxonomic-levels |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| plot |
../../Tools/qiime/plot_taxa_summary.cwl
(CommandLineTool)
|
||
| cluster |
../../Tools/qiime/pick_de_novo_otus.cwl
(CommandLineTool)
|
||
| taxonomy |
../../Tools/qiime/assign_taxonomy.cwl
(CommandLineTool)
|
||
| otu-table |
../../Tools/qiime/make_otu_table.cwl
(CommandLineTool)
|
||
| sort-table |
../../Tools/qiime/sort_otu_table.cwl
(CommandLineTool)
|
||
| filter-otus |
../../Tools/qiime/filter_otus_from_otu_table.cwl
(CommandLineTool)
|
||
| summarize_taxa |
../../Tools/qiime/summarize_taxa.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| plots | Directory | ||
| errors | File[] | ||
| results | File[] (Optional) |
Permalink:
https://w3id.org/cwl/view/git/4304c60b6e2e7980ad1d659f4b904730ce9c0706/CWL/Workflows/qiime/demultiplexed-fasta2taxa-summary-plot.cwl
