Workflow: abundance
Fetched 2023-01-12 22:41:24 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 | ||
| m5nrSCG | File | ||
| coverage | File (Optional) | ||
| md5index | File | ||
| expandSims | File[] | ||
| filterSims | File[] | ||
| rnaClustMap | File | ||
| protClustMap | File | ||
| rnaExpandLca | File | ||
| protExpandLca | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| lcaProfile |
contig-lca.workflow.cwl
(Workflow)
|
contig LCA |
create LCA consistant across input contigs contigs order of precedence - rRNA, single copy gene, LCA of genes |
| 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/2addcde0f4c1c8547f7f3906c2523cded23e9869/CWL/Workflows/abundance-clca.workflow.cwl
