Workflow: abundance

Fetched 2023-01-13 05:31:19 GMT

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

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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs rnaExpandLca rnaExpandLca lcaProfile contig LCA rnaExpandLca->lcaProfile rnaExpandLca filterSims filterSims md5Profile abundance profile filterSims->md5Profile input rnaClustMap rnaClustMap rnaClustMap->md5Profile cluster sourceStats abundance profile rnaClustMap->sourceStats cluster rnaClustMap->lcaProfile rnaClustMap coverage coverage coverage->md5Profile coverage coverage->sourceStats coverage coverage->lcaProfile coverage jobid jobid jobid->md5Profile outName jobid->sourceStats outName jobid->lcaProfile jobid m5nrSCG m5nrSCG m5nrSCG->lcaProfile m5nrSCG protExpandLca protExpandLca protExpandLca->lcaProfile protExpandLca expandSims expandSims expandSims->sourceStats input md5index md5index md5index->md5Profile md5index protClustMap protClustMap protClustMap->md5Profile cluster protClustMap->sourceStats cluster protClustMap->lcaProfile protClustMap lcaProfileOut lcaProfileOut sourceStatsOut sourceStatsOut md5ProfileOut md5ProfileOut md5Profile->md5ProfileOut sourceStats->sourceStatsOut lcaProfile->lcaProfileOut
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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/091374dc59a23966338638a668ae397d4ee20b2f/CWL/Workflows/abundance-clca.workflow.cwl