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Shiny File Process Specifications

Process Details

  • Name: shiny_file_process
  • Process UUID: f931lffbevyl3u22fmq5moja6osal3
  • Process Group: short_read_taxonomy

Overview

This process prepares required files for animalcules and microviz applications in taxonomic analysis workflows. It processes taxonomic data and metadata to generate properly formatted files that can be used by downstream Shiny-based visualization and analysis tools for microbiome studies.

This process is implemented in Bash, which invokes R scripts for data preparation and file formatting.

Key Functionality

  • File Preparation for Animalcules: Formats taxonomic data and reads for use in the animalcules Shiny application
  • Optional MicroViz Support: Conditionally prepares files for microviz visualization when enabled
  • Metadata Integration: Processes and integrates metadata files with taxonomic data for comprehensive analysis

Input/Output Specification

Inputs

Required Inputs

  • Input Directory

    • Description: Directory containing input files for processing
    • Format: Directory

  • Input Text File (Reads)

    • Description: Text file containing sequencing reads data
    • Format: TXT

  • Input Text File (Taxonomy Database)

    • Description: Text file containing taxonomic classification database
    • Format: TXT

Outputs

  • Output Text Files

    • Description: Processed text files formatted for animalcules and microviz applications
    • Format: TXT

  • Gene Dependency Scores

    • Description: R data structure containing processed dependency scores
    • Format: RDS

References & Resources

  • Tool Documentation: Contact the team for details on animalcules_file_prep.R and microViz_file_prep.R
  • Related Papers: McMurdie, Paul J., and Susan Holmes. "phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data." PLoS one 8.4 (2013): e61217.