class: GalaxyWorkflowDraft
label: Ebola Virus Infection RNA-seq Analysis (A549 WT vs PTPN13-KO)
doc: Transcript quantification with Salmon followed by multi-factor differential expression analysis with DESeq2 for paired-end RNA-seq from human A549 WT and A549 PTPN13-KO cells infected with Ebola virus vs mock infection at 24 and 48 HPI.
inputs:
  reads_paired_collection:
    type: collection
    collection_type: list:paired
    format: fastqsanger.gz
    doc: Paired-end Illumina RNA-seq reads across experimental samples
  salmon_index:
    type: data
    format: fasta
    doc: Reference transcriptome FASTA for Salmon quantification
  sample_metadata:
    type: data
    format: tabular
    doc: Tabular sample metadata specifying Genotype, Condition, and Timepoint
  tx2gene_map:
    type: data
    format: tabular
    doc: Tabular mapping between transcript identifiers and gene identifiers
outputs:
  salmon_quant_collection:
    outputSource: salmon_quant/output_quant
    doc: Per-sample Salmon transcript abundance and count tables
  deseq2_norm_counts:
    outputSource: deseq2/counts_out
    doc: DESeq2 normalized counts matrix across all samples
  deseq2_differential_results:
    outputSource: deseq2/deseq_out
    doc: DESeq2 differential expression results table
  deseq2_plots:
    outputSource: deseq2/plots
    doc: DESeq2 QC and diagnostic plots (PCA, dispersion)
steps:
  salmon_quant:
    tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy5
    tool_version: 1.10.1+galaxy5
    label: Quantify transcripts with Salmon
    tool_shed_repository:
      changeset_revision: 29e12b90949d
      name: salmon
      owner: bgruening
      tool_shed: toolshed.g2.bx.psu.edu
    in:
      quant_type|input|single_or_paired|input_1: reads_paired_collection
      quant_type|refTranscriptSource|s_index|fasta: salmon_index
    out:
      - id: output_quant
    tool_state:
      quant_type:
        qtype: reads
        input:
          single_or_paired:
            single_or_paired_opts: paired_collection
            libtype:
              strandedness: A
        refTranscriptSource:
          TranscriptSource: history
          s_index:
            kmer: 31
  deseq2:
    tool_id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3
    tool_version: 2.11.40.8+galaxy3
    label: Differential gene expression analysis with DESeq2
    tool_shed_repository:
      changeset_revision: b060944b3989
      name: deseq2
      owner: iuc
      tool_shed: toolshed.g2.bx.psu.edu
    in:
      select_data|countsFile: salmon_quant/output_quant
      select_data|sample_sheet: sample_metadata
      tximport|mapping_format|tabular_file: tx2gene_map
    out:
      - id: counts_out
      - id: deseq_out
      - id: plots
    tool_state:
      select_data:
        how: sample_sheet_contrasts
        design_formula_mode:
          mode: custom
          design_formula: "~ Condition"
      tximport:
        tximport_selector: tximport
        txtype: salmon
        mapping_format:
          mapping_format_selector: tabular
      output_options:
        output_selector:
          - pdf
          - normCounts