Workflow: Run taxonomic classification, create OTU table and krona visualisation
Fetched 2024-05-20 03:40:29 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| fasta | File | ||
| otu_ref | String | ||
| otu_label | String | ||
| mapseq_ref | File | ||
| return_dirname | String | ||
| file_for_prefix | File | ||
| mapseq_taxonomy | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mapseq |
../../tools/RNA_prediction/mapseq/mapseq.cwl
(CommandLineTool)
|
MAPseq v 1.2.3 |
sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. https://github.com/jfmrod/MAPseq |
| counts_to_hdf5 |
../../tools/RNA_prediction/biom-convert/biom-convert.cwl
(CommandLineTool)
|
||
| counts_to_json |
../../tools/RNA_prediction/biom-convert/biom-convert.cwl
(CommandLineTool)
|
||
| compress_mapseq |
../../utils/pigz/gzip.cwl
(CommandLineTool)
|
||
| return_output_dir |
../../utils/return_directory.cwl
(ExpressionTool)
|
||
| count_lines_mapseq |
../../utils/count_number_lines.cwl
(CommandLineTool)
|
||
| visualize_otu_counts |
../../tools/RNA_prediction/krona/krona.cwl
(CommandLineTool)
|
visualize using krona | |
| classifications_to_otu_counts |
../../tools/RNA_prediction/mapseq2biom/mapseq2biom.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| out_dir | Directory (Optional) | ||
| number_lines_mapseq | Integer |
Permalink:
https://w3id.org/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/workflows/subworkflows/classify-otu-visualise.cwl
