data.yml

id: data
title: Data import and preparation
tabs:
  - id: tools
    title: Tools
    heading_html: >
      Common tools are listed here, or search for more in the full tool panel to the left.
    content:
      - title_html: Import data to Galaxy
        description_html: >
          <p>
            Standard upload of data to Galaxy, from your computer or from the web.
          </p>
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
      - title_html: <code>FastQC</code> - sequence quality reports
        description_html: >
          <p>
            Before using your sequencing data, it's important first ensure that the data quality is sufficient for your analysis.
          </p>
        inputs:
          - datatypes:
              - fastq
              - bam
              - sam
        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc"
      - title_html: <code>FastP</code> - sequence quality reports, trimming & filtering
        description_html: >
          <p>
            Faster run than FastQC, this tool can also trim reads and filter by quality.
          </p>
  - id: workflows
    title: Workflows
    heading_html: >
      A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
      <a href="https://galaxyproject.org/learn/advanced-workflow/" target="_blank">Learn more.</a>
    content:
      - title_html: Data QC
        description_html: >
          <p>
            Report statistics from sequencing reads. <br> <br> Tools: <code>nanoplot</code> <code>fastqc</code> <code>multiqc</code>
          </p>
        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
        view_link: https://workflowhub.eu/workflows/222
        view_tip: View in WorkflowHub
        button_tip: Import to Galaxy AU
      - title_html: Trim and filter reads
        description_html: >
          <p>
            Trims and filters raw sequence reads according to specified settings. <br> <br> Tools: <code>fastp</code>
          </p>
        button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=224"
        view_link: https://workflowhub.eu/workflows/224
        view_tip: View in WorkflowHub
        button_tip: Import to Galaxy AU
  - id: help
    title: Help
    content:
      - title_html: How can I import my Single Cell data?
        description_html: >
          <p>
            You can upload your data to Galaxy using the Upload tool from anywhere in Galaxy. Just look for the "Upload data" button at the top of the tool panel.
          </p>
        button_html: More info
        button_link: https://training.galaxyproject.org/training-material/topics/galaxy-interface/
      - title_html: How can I subsample my data?
        description_html: >
          <p>
            We recommend subsampling large data sets to test tools and workflows. A useful tool is <code>seqtk_seq</code>, setting the parameter at "Sample fraction of sequences".
          </p>
      - title_html: Can I upload sensitive data?
        description_html: >
          <p>
            No, do not upload personal or sensitive, such as human health or clinical data. Please see our <a href="/about#data-privacy">Data Privacy</a> page for definitions of sensitive and health-related information.
          </p>
          <p>
            Please also make sure you have read our <a href="/about#terms-of-service">Terms of Service</a>, which covers hosting and analysis of research data.
          </p>
      - title_html: Is my data private?
        description_html: >
          <p>
            Please read our <a href="/about#data-privacy">Privacy Policy</a> for information on your personal data and any data that you upload.
          </p>
      - title_html: How can I increase my storage quota?
        description_html: >
          <p>
            Please submit a quota request if your Galaxy Australia account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
          </p>
        button_html: Request
        button_link: /request/quota
      - title_html: "Tutorial: Quality Control"
        description_html: >
          <p>
            Quality control and data cleaning is an essential first step in any NGS analysis. This tutorial will show you how to use and interpret results from <code>FastQC</code>, <code>NanoPlot</code> and <code>PycoQC</code>.
          </p>
        button_html: Tutorial
        button_link: https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html
      - title_html: "Tutorial: introduction to Genomics and Galaxy"
        description_html: >
          <p>
            This practical aims to familiarize you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work.
          </p>
        button_html: Tutorial
        button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html
      - title_html: Galaxy Australia support
        description_html: >
          <p>
            Any user of Galaxy Australia can request support through an online form.
          </p>
        button_html: Request support
        button_link: /request/support