Importing via links

Authors:

Bérénice Batut

Helena Rasche

Mehmet Tekman

Gildas Le Corguillé

Saskia Hiltemann

Wendi Bacon

Anton Nekrutenko

Maria Doyle Add Contributions!

Copy the link location
Click galaxy-upload Upload Data at the top of the tool panel
Select galaxy-wf-edit Paste/Fetch Data
Paste the link(s) into the text field
Press Start
Close the window

Persistent URL

Resource PURL: https://gxy.io/GTN:F00040

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Want to embed this snippet (FAQ) in your GTN Tutorial?

{% snippet  faqs/galaxy/datasets_import_via_link.md %}

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:

{% snippet faqs/galaxy/datasets_import_via_link.md collection="true" collection_type="List" collection_name="raw_files" format="thermo.raw"  %}

Create a paired collection with a given naming scheme:

{% snippet faqs/galaxy/datasets_import_via_link.md 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:

{% snippet faqs/galaxy/datasets_import_via_link.md link="https://zenodo.org/record/3254917/files/chr21.gtf" format="interval" genome="mm9"  %}

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