datasets_import_via_link.md

---

title: Importing via links
area: data upload
box_type: tip
layout: faq
contributors: [bebatut,hexylena,mtekman,lecorguille,shiltemann,nomadscientist,nekrut,mblue9]
optional_parameters:
  reset_form: Tell the user to reset the form first
  collection: Adds step to click the collection button
  collection_type: Suggests a collection type
  link: (Deprecated) Instead of collections use a link-type input
  link2: (Deprecated) Second link
  format: Suggests a format for the user to set
  genome: Suggests a genome for the user to set
  pairswaptext: Provides a filter for the pair detection
  collection_name_convention: Suggests a naming convention for the collection
examples:
  Import a list of files:
    collection: 'true'
    collection_type: List
    collection_name: raw_files
    format: thermo.raw
  Create a paired collection with a given naming scheme:
    collection: 'true'
    collection_type: Paired
    collection_name_convention: "'<name>_<plate>_<batch>' to preserve the sample names, sequencing plate number and batch number."
    collection_name: "Here we will write 'C57_P1_B1'"
    genome: "GRCm38/mm10"
    pairswaptext: "'SRR5683689_1' and 'SRR5683689_2'"
  "Import an interval file with specified genome, though providing the links in a code block is preferred":
    link: "https://zenodo.org/record/3254917/files/chr21.gtf"
    format: interval
    genome: mm9

---

• Copy the link location

• Click {% icon galaxy-upload %} Upload at the top of the activity panel {% if include.reset_form %}

• Click Reset button at the bottom of the form. If the button is greyed out -> skip to the next step. {% endif %} {% if include.collection %}

• Click on Collection on the top {% endif %} {% if include.collection_type %}

• Click on Collection Type and select {{ include.collection_type }} {% endif %}

• Select {% icon galaxy-wf-edit %} Paste/Fetch Data

• Paste the link(s) into the text field {% if include.link %} {{ include.link }} {% endif %} {% if include.link2 %} {{ include.link2 }} {% endif %} {% if include.format %}

• Change Type (set all): from "Auto-detect" to {{ include.format }} {% endif %} {% if include.genome %}

• Change Genome to {{ include.genome }} {% endif %}

• Press Start {% if include.collection %}

• Click on Build when available {% if include.pairswaptext %}

• Ensure that the forward and reverse reads are set to {{ include.pairswaptext }}, respectively.

  • Click Swap otherwise {% endif %}

• Enter a name for the collection {% if include.collection_name_convention %}

  • A useful naming convention is to use {{ include.collection_name_convention }} {% endif %} {% if include.collection_name %}

  • {{ include.collection_name }} {% endif %}

• Click on Create list (and wait a bit) {% else %}

• Close the window {% endif %}