class: GalaxyWorkflow
label: DESeq2 Differential Expression Subgraph
inputs:
  - id: counts_collection
    type: collection
    collection_type: list
    optional: false
    doc: Collection of count/abundance tables across samples
  - id: sample_metadata
    type: data
    optional: false
    doc: Tabular sample metadata specifying experimental factors
outputs:
  - id: deseq2_plots
    outputSource: deseq2/plots
  - id: deseq2_norm_counts
    outputSource: deseq2/counts_out
  - id: deseq2_results
    outputSource: deseq2/deseq_out
steps:
  - id: deseq2
    label: Differential Analysis
    tool_id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3
    tool_version: 2.11.40.8+galaxy3
    tool_shed_repository:
      changeset_revision: b060944b3989
      name: deseq2
      owner: iuc
      tool_shed: toolshed.g2.bx.psu.edu
    in:
      - id: select_data|countsFile
        source: counts_collection
    out:
      - id: deseq_out
      - id: counts_out
      - id: plots
    tool_state:
      output_options:
        output_selector:
          - pdf
          - normCounts
      select_data:
        how: datasets_per_level
        __current_case__: 1