CWL Workflow: fasta2taxa-plot

Workflow: fasta2taxa-plot

Fetched 2023-01-12 10:56:06 GMT

Verified with cwltool version 3.1.20221201130942

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.

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Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: GNU General Public License v3.0 only

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
sample-mapping	File
fasta-demultiplexed	File
min-observations-per-otu	Integer (Optional)
min-observations-per-sample	Integer (Optional)
summarize-for-taxonomic-levels

Steps

ID	Runs	Label	Doc
cluster	../../Tools/qiime/pick_de_novo_otus.cwl (CommandLineTool)
taxonomy	../../Tools/qiime/assign_taxonomy.cwl (CommandLineTool)
otu-table	../../Tools/qiime/make_otu_table.cwl (CommandLineTool)
sort-table	../../Tools/qiime/sort_otu_table.cwl (CommandLineTool)
filter-otus	../../Tools/qiime/filter_otus_from_otu_table.cwl (CommandLineTool)
beta-diversity	../../Tools/qiime/beta_diversity_through_plots.cwl (CommandLineTool)
filter-samples	../../Tools/qiime/filter_samples_from_otu_table.cwl (CommandLineTool)
summarize-taxa	../../Tools/qiime/summarize_taxa.cwl (CommandLineTool)
alpha-diversity	../../Tools/qiime/alpha_diversity.cwl (CommandLineTool)
plot-taxa-summary	../../Tools/qiime/plot_taxa_summary.cwl (CommandLineTool)

Outputs

ID	Type	Doc
results	Directory[]
error-logs	File[]	Error logs for each step, collected by default and can be empty.
taxa-summary-plots	Directory
beta-diversity-results	Directory
aplha-diversity-results	File