Workflow: abundance
Fetched 2025-11-08 20:43:36 GMT
Verified with cwltool version 3.1.20221201130942
abundace profiles from annotated files, for protein and/or rna
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| jobid | String | ||
| lcaAnns | File[] | ||
| coverage | File (Optional) | ||
| md5index | File | ||
| clustMaps | File[] | ||
| expandSims | File[] | ||
| filterSims | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| lcaProfile |
../Tools/sims_abundance.tool.cwl
(CommandLineTool)
|
abundance profile |
create abundance profile from expanded annotated sims files md5: sims_abundance.py -t md5 -i <input> -o <output> --coverage <coverage> --cluster <cluster> --md5index <md5index> lca: sims_abundance.py -t lca -i <input> -o <output> --coverage <coverage> --cluster <cluster> source: sims_abundance.py -t source -i <input> -o <output> --coverage <coverage> --cluster <cluster> |
| md5Profile |
../Tools/sims_abundance.tool.cwl
(CommandLineTool)
|
abundance profile |
create abundance profile from expanded annotated sims files md5: sims_abundance.py -t md5 -i <input> -o <output> --coverage <coverage> --cluster <cluster> --md5index <md5index> lca: sims_abundance.py -t lca -i <input> -o <output> --coverage <coverage> --cluster <cluster> source: sims_abundance.py -t source -i <input> -o <output> --coverage <coverage> --cluster <cluster> |
| sourceStats |
../Tools/sims_abundance.tool.cwl
(CommandLineTool)
|
abundance profile |
create abundance profile from expanded annotated sims files md5: sims_abundance.py -t md5 -i <input> -o <output> --coverage <coverage> --cluster <cluster> --md5index <md5index> lca: sims_abundance.py -t lca -i <input> -o <output> --coverage <coverage> --cluster <cluster> source: sims_abundance.py -t source -i <input> -o <output> --coverage <coverage> --cluster <cluster> |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| lcaProfileOut | File | ||
| md5ProfileOut | File | ||
| sourceStatsOut | File |
https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance.workflow.cwl
