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User Guide

Table of Contents

  1. Introduction
  2. Installation
    1. Requirements
    2. Downloading
    3. Setup and launching
  3. Interface overview
    1. Server library
    2. Personal library
    3. Workflow area
    4. Connection manager
    5. Provenance editor
    6. Preferences
    7. Search feature
    8. Checking for latest updates
    9. Starting GUI from command line
    10. Running from the command line
  4. Building a workflow
    1. Dragging in modules
    2. Connecting modules
      1. Smartline
    3. Setting parameter values
    4. Data sources and data sinks
    5. Study module
      1. Input data tab
      2. Grouping tab
      3. Matrix tab
    6. Conditionals
      1. File conditions example
      2. Arithmetical/Comparison example
      3. Metadata conditions example
    7. Web service modules
    8. Remote file browser
    9. Processing multiple inputs
    10. Enable/Disable parameters
    11. Annotations
    12. Variables
    13. IDA
    14. XNAT
    15. Server changer
    16. Grammar view
  5. Execution
    1. Validation
    2. Executing a workflow
    3. Client disconnect/reconnect
    4. Server status
    5. Pausing a workflow
    6. Stopping a workflow
    7. Restart a module
    8. Module statuses
    9. Viewing output
    10. Debugging execution
    11. Report a bug
  6. Creating modules
    1. Simple modules
      1. Info tab
        1. General module information
        2. Citation information
      2. Parameters tab
        1. General parameter information
        2. Parameter types
        3. File types
        4. Parameter arguments size
        5. Advanced parameter information
          1. Select dependencies
          2. Transformations
          3. Output/Error stream extraction
          4. Metadata extraction
      3. Execution tab
        1. Executable location
        2. Advanced options
      4. Metadata tab – Metadata Augmentation
    2. Module groups
  7. Advanced Topics
    1. Syncing Execution Flow
    2. Exporting Pipeline Workflow to Script
    3. Remote GUI Invocation
    4. Workflow Diff Utility