Workflow: abundance
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/6c5d0068bdb4f19a36a653c39964aefb9e5a7b1b/CWL/Workflows/abundance-clca.workflow.cwl