Workflow: qiime2 identify differentially abundant features
Fetched 2024-04-27 04:27:13 GMT
Verified with cwltool version 3.1.20221201130942
Differential abundance testing with ANCOM from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/
- Selected
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- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| table | File | ||
| taxonomy | File | ||
| collapse_level | Integer | ||
| sample_metadata | File | ||
| filter_sample_query | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| ancom_subject_16 |
qiime2-step2-dada2.cwl#composition-ancom.cwl
(CommandLineTool)
|
qiime2: Apply ANCOM to identify features that are differentially abundant across groups | |
| comp_gut_table_l6 |
qiime2-step2-dada2.cwl#composition-add-pseudocount.cwl
(CommandLineTool)
|
qiime2: Increment all counts in table by pseudocount | |
| filter_gut_samples |
qiime2-step2-dada2.cwl#feature-table-filter-samples.cwl
(CommandLineTool)
|
qiime2: Filter samples from table based on frequency and/or metadata | |
| gut_table_collapse |
qiime2-step2-dada2.cwl#taxa-collapse.cwl
(CommandLineTool)
|
qiime2: Collapse groups of features that have the same taxonomic assignment through the specified level | |
| pseudocount_gut_table |
qiime2-step2-dada2.cwl#composition-add-pseudocount.cwl
(CommandLineTool)
|
qiime2: Increment all counts in table by pseudocount | |
| ancom_subject_column_gut_table |
qiime2-step2-dada2.cwl#composition-ancom.cwl
(CommandLineTool)
|
qiime2: Apply ANCOM to identify features that are differentially abundant across groups |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filter_table_file | File | ||
| collapsed_table_file | File | ||
| comp_gut_table_l6_file | File | ||
| composition_table_file | File | ||
| ancom_visualization_file | File | ||
| ancom_subject_16_visualization_file | File |
Permalink:
https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/qiime2-step2-dada2.cwl?part=qiime2-09-ancom.cwl
