Workflow: qiime2 diversity analyses
Fetched 2024-11-26 05:04:42 GMT
Verified with cwltool version 3.1.20221201130942
Alpha and beta diversity analysis
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 | ||
| rooted_tree | File | ||
| sampling_depth | Integer | ||
| sample_metadata | File | ||
| rarefied_table_filename | String | ||
| shannon_vector_filename | String | ||
| evenness_vector_filename | String | ||
| faith_pd_vector_filename | String | ||
| jaccard_emperor_filename | String | ||
| bray_curtis_emperor_filename | String | ||
| jaccard_pcoa_results_filename | String | ||
| observed_otus_vector_filename | String | ||
| jaccard_distance_matrix_filename | String | ||
| bray_curtis_pcoa_results_filename | String | ||
| weighted_unifrac_emperor_filename | String | ||
| unweighted_unifrac_metadata_column | String | ||
| shannon_group_significance_filename | String | ||
| unweighted_unifrac_emperor_filename | String | ||
| bray_curtis_distance_matrix_filename | String | ||
| evenness_group_significance_filename | String | ||
| faith_pd_group_significance_filename | String | ||
| weighted_unifrac_pcoa_results_filename | String | ||
| unweighted_unifrac_pcoa_results_filename | String | ||
| unweighted_unifrac_significance_filename | String | ||
| weighted_unifrac_distance_matrix_filename | String | ||
| unweighted_unifrac_distance_matrix_filename | String | ||
| unweighted_unifrac_body_site_significance_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| generate_core_metrics |
../tools/qiime2/diversity-core-metrics-phylogenetic.cwl
(CommandLineTool)
|
qiime2: Applies a collection of diversity metrics (both phylogenetic and non-phylogenetic) to a feature table. | |
| shannon_group_significance |
../tools/qiime2/diversity-alpha-group-significance.cwl
(CommandLineTool)
|
qiime2: Visually and statistically compare groups of alpha diversity values | |
| evenness_group_significance |
../tools/qiime2/diversity-alpha-group-significance.cwl
(CommandLineTool)
|
qiime2: Visually and statistically compare groups of alpha diversity values | |
| faith_pd_group_significance |
../tools/qiime2/diversity-alpha-group-significance.cwl
(CommandLineTool)
|
qiime2: Visually and statistically compare groups of alpha diversity values | |
| unweighted_unifrac_significance |
../tools/qiime2/diversity-beta-group-significance.cwl
(CommandLineTool)
|
qiime2: Determine whether groups of samples are significantly different from one another using a permutation-based statistical test |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| rarefied_table | File | ||
| shannon_vector | File | ||
| evenness_vector | File | ||
| faith_pd_vector | File | ||
| jaccard_emperor | File | ||
| bray_curtis_emperor | File | ||
| jaccard_pcoa_results | File | ||
| observed_otus_vector | File | ||
| jaccard_distance_matrix | File | ||
| bray_curtis_pcoa_results | File | ||
| weighted_unifrac_emperor | File | ||
| unweighted_unifrac_emperor | File | ||
| bray_curtis_distance_matrix | File | ||
| weighted_unifrac_pcoa_results | File | ||
| shannon_group_significance_file | File | ||
| unweighted_unifrac_pcoa_results | File | ||
| evenness_group_significance_file | File | ||
| faith_pd_group_significance_file | File | ||
| weighted_unifrac_distance_matrix | File | ||
| unweighted_unifrac_distance_matrix | File | ||
| unweighted_unifrac_significance_file | File |
Permalink:
https://w3id.org/cwl/view/git/a6a7d5bd034f8ccf01b809bc9f5ecf87e5c5652c/subworkflows/qiime2-paired-alpha-beta-diversity.cwl
