Workflow: qiime2 identify differentially abundant features

Fetched 2024-02-28 06:23:57 GMT

Differential abundance testing with ANCOM from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

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Inputs

ID Type Title Doc
table File
taxonomy File
collapse_level Integer
sample_metadata File
filter_sample_query String

Steps

ID Runs Label Doc
ancom_subject_16
qiime2-step2-dada2.cwl#composition-ancom.cwl (CommandLineTool)
qiime2: Apply ANCOM to identify features that are differentially abundant across groups
comp_gut_table_l6
qiime2-step2-dada2.cwl#composition-add-pseudocount.cwl (CommandLineTool)
qiime2: Increment all counts in table by pseudocount
filter_gut_samples
qiime2-step2-dada2.cwl#feature-table-filter-samples.cwl (CommandLineTool)
qiime2: Filter samples from table based on frequency and/or metadata
gut_table_collapse
qiime2-step2-dada2.cwl#taxa-collapse.cwl (CommandLineTool)
qiime2: Collapse groups of features that have the same taxonomic assignment through the specified level
pseudocount_gut_table
qiime2-step2-dada2.cwl#composition-add-pseudocount.cwl (CommandLineTool)
qiime2: Increment all counts in table by pseudocount
ancom_subject_column_gut_table
qiime2-step2-dada2.cwl#composition-ancom.cwl (CommandLineTool)
qiime2: Apply ANCOM to identify features that are differentially abundant across groups

Outputs

ID Type Label Doc
filter_table_file File
collapsed_table_file File
comp_gut_table_l6_file File
composition_table_file File
ancom_visualization_file File
ancom_subject_16_visualization_file File
Permalink: https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/qiime2-step2-dada2.cwl?part=qiime2-09-ancom.cwl