Workflow: abundance

Fetched 2023-01-14 18:23:42 GMT

abundace profiles from annotated files, for protein and/or rna

children parents
Workflow as SVG
  • 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

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
Permalink: https://w3id.org/cwl/view/git/9aba38fd1569287b7256ace7163ac84320909f8a/CWL/Workflows/abundance-clca.workflow.cwl