Workflow: contig LCA
Fetched 2023-01-04 06:23:11 GMT
Verified with cwltool version 3.1.20221201130942
create LCA consistant across input contigs contigs order of precedence - rRNA, single copy gene, LCA of genes
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| jobid | String | ||
| m5nrSCG | File | ||
| coverage | File (Optional) | ||
| rnaClustMap | File | ||
| protClustMap | File | ||
| rnaExpandLca | File | ||
| protExpandLca | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sortRna |
../Tools/sort.tool.cwl
(CommandLineTool)
|
GNU sort |
sort text file base on given field(s) |
| sortProt |
../Tools/sort.tool.cwl
(CommandLineTool)
|
GNU sort |
sort text file base on given field(s) |
| expandLca |
../Tools/find_contig_lca.tool.cwl
(CommandLineTool)
|
contig LCA |
create contig LCA from rRNA and Protein LCAs >find_contig_lca.py --rna <rnaLCA> --prot <protLCA> --scg <scgs> --output <outName> |
| abundanceLca |
../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> |
| unclusterRna |
../Tools/uncluster_sims.tool.cwl
(CommandLineTool)
|
uncluster sims |
expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member >uncluster_sims.py <input> <outName> --cfile <cluster> --position <position> |
| unclusterProt |
../Tools/uncluster_sims.tool.cwl
(CommandLineTool)
|
uncluster sims |
expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member >uncluster_sims.py <input> <outName> --cfile <cluster> --position <position> |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| contigLCA | File |
https://w3id.org/cwl/view/git/6c5d0068bdb4f19a36a653c39964aefb9e5a7b1b/CWL/Workflows/contig-lca.workflow.cwl
