Advanced uses of Galaxy often require the use of dataset collections, which can contain between one and tens of thousands of datasets. Grouping datasets in this way has numerous advantages:

• It is easy to represent a single collection in the History
• Dataset names (“Element Identifiers”) are immutable and preserved
• Collections can be split and nested in arbitrary ways

While collections can be split in any way, doing so for multi-factor analysis quickly becomes cumbersome and messy. An alternative is to label collection elements with special group tags, i.e. tags prefixed by the string group:. Note that group tags currently do not propagate, i.e. they are not inherited to datasets resulting from analyses. These tags can be displayed in the Tool form, allowing users to select subsets of collections.

This tutorial outlines how to set and use group tags with the DESeq2 tool. For a more detailed description and background for differential expression testing see the Reference-based RNA-Seq data analysis.

Agenda

In this tutorial, we will cover:

1. Setting group tags using the apply rules tool
   1. Set group tags during upload
   2. Set group tags using the “Tag elements from file” tool
2. Using group tags in tool, e.g. DESeq2
3. Conclusion

Setting group tags using the apply rules tool

There are several ways to set group tags:

• Using the Rule Based Uploader
• Using the “Tag elements from file” tool
• Using the “Apply Rules” tool
• Manually adding dataset tags with the prefix group:

We will use the first two methods in this tutorial. The second and third methods work at any step during the analysis. Note that the function of the “Apply Rules” tool is (nearly) identical to the Rule Based Uploader.

Set group tags during upload

Hands On: Set group tags during upload

1. Create a new history for this tutorial

   Tip: Creating a new history

   To create a new history simply click the new-history icon at the top of the history panel:

   

2. Open the Galaxy Upload Manager (galaxy-upload on the top-right of the tool panel)

3. Click on Rule-based on the top

   

   As you can see in this dialog, data can be selected from a history dataset or pasted in directly

4. Set Upload data as: to Collection(s)

5. Paste the following links into the text box

   https://zenodo.org/record/1185122/files/GSM461176_untreat_single.counts
   https://zenodo.org/record/1185122/files/GSM461177_untreat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461178_untreat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461179_treat_single.counts
   https://zenodo.org/record/1185122/files/GSM461180_treat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461181_treat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461182_untreat_single.counts
   

6. Click Build
7. We will add a regex that creates 3 new columns with accession, treatment and library type:
   • Click on the Column button and then Using a Regular Expression
   • Select Create columns matching expression groups
   • Paste .*(GSM.*)_(.*)_(.*).counts in “Regular Expression”
   • Set “Number of Groups” to 3

   • Click on Apply

     We should have now a table with 4 columns: link, sample name, treatment, sequencing type

   • Click on Rules and then Add / Modify Column Definitions
   • Click on Add Definition and select:
     • “URL”: Column A (Note that this option is absent when using the “Apply rules tool”)
     • “List Identifiers”: Column B
     • “Group Tags”: Columns C and D (Select Column C first and then add D by clicking on “… Add another column”)
   • Click Apply
   • Enter a name for the new collection
   • Click Upload

8. Expand the generated collection and the files in it and check their names and tags

   

Set group tags using the “Tag elements from file” tool

We now want to add group tags using the “Tag elements from file” tool.

Hands On: Upload and create a collection

1. Create a new history for this tutorial

2. Import the following files

   https://zenodo.org/record/1185122/files/GSM461176_untreat_single.counts
   https://zenodo.org/record/1185122/files/GSM461177_untreat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461178_untreat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461179_treat_single.counts
   https://zenodo.org/record/1185122/files/GSM461180_treat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461181_treat_paired.counts
   https://zenodo.org/record/1185122/files/GSM461182_untreat_single.counts
   

   Tip: Importing via links

   • 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

3. Create a Dataset List (Collection) with these 7 files

   Tip: Creating a dataset collection

   • Click on galaxy-selector Select Items at the top of the history panel
   • Check The 7 datasets you’ve just imported

   • Click 7 of N selected and choose Build Dataset List

     

   • Enter a name for your collection
   • Click Create list to build your collection
   • Click on the checkmark icon at the top of your history again

We have now a collection with our files. We can now either upload a tabular file containing the element identifiers and the tags we want to apply, or we can extract the element identifiers and extract the tags using a Regular Expression. We will do the latter.

Hands On: Set group tags using the "Tag elements from file" tool

1. Extract element identifiers tool
   • param-collection “Dataset collection”: created collection
2. Replace Text in entire line tool
   • param-file “File to process”: output of Extract element identifiers tool
   • In “Replacement”:
     • In “1: Replacement”
       • “Find pattern”: (.*)_(.*)_(.*).counts
       • “Replace with”: \1_\2_\3.counts\tgroup:\2\tgroup:\3

   This step adds an additional columns that can be used with the Tag elements from file tool

3. Change the datatype to tabular

   Tip: Changing the datatype

   • Click on the galaxy-pencil pencil icon for the dataset to edit its attributes
   • In the central panel, click galaxy-chart-select-data Datatypes tab on the top
   • In the galaxy-chart-select-data Assign Datatype, select tabular from “New Type” dropdown
     • Tip: you can start typing the datatype into the field to filter the dropdown menu
   • Click the Save button

4. Tag elements from file tool
   • param-collection “Input Collection”: created collection
   • param-collection “Tag collection elements according to this file”: output of Replace Text tool

You should now have a properly tagged collection of tabular files that can be used in DESeq2.

Using group tags in tool, e.g. DESeq2

DESeq2 has two modes for specifying factors. One can either select datasets corresponding to factors, or use group tags to specify factors. We will use the group tags present in our collection to specify factors.

The tool interface will prompt you with the group tags that are available for your inputs:

Hands On: Running DESeq2 with group tags

1. DESeq2 tool with the following parameters:
   • “how”: Select group tags corresponding to levels
     • param-collection “Count file(s) collection”: Generated collection
     • In “Factor”:
       • In “1: Factor”
         • “Specify a factor name”: Treatment
         • In “Factor level”:
           • In “1: Factor level”:
             • “Specify a factor level”: treat
             • “Select groups that correspond to this factor level”: Tags: treat
           • In “2: Factor level”:
             • “Specify a factor level”: untreat
             • “Select groups that correspond to this factor level”: Tags: untreat
       • Click on param-repeat “Insert Factor” (not on “Insert Factor level”)
       • In “2: Factor”
         • “Specify a factor name” to Sequencing
         • In “Factor level”:
           • In “1: Factor level”:
             • “Specify a factor level”: paired
             • “Select groups that correspond to this factor level”: Tags: paired
           • In “2: Factor level”:
             • “Specify a factor level”: single
             • “Select groups that correspond to this factor level”: Tags: single
   • “Files have header?”: No
   • “Output normalized counts table”: Yes

Conclusion

We can select a subset of Collections using the special group tag.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Group tags allow complex analyses without reshaping or unhiding datasets in a collection

Frequently Asked Questions

• Tutorial FAQs
• Topic FAQs
• Galaxy FAQs
• GTN Matrix Chat
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Feedback

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Citing this Tutorial

1. Marius van den Beek, Group tags for complex experimental designs (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/group-tags/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{galaxy-interface-group-tags,
author = "Marius van den Beek",
	title = "Group tags for complex experimental designs (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/group-tags/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

Feedback

t{ hist[0] | to_stars }}	1
t{ hist[0] | to_stars }}	3
t{ hist[0] | to_stars }}	1
t{ hist[0] | to_stars }}	1

November 2023

• 1 stars: Disliked: I'm trying to use data from GEO and there are no tags nor a tag file. I can't figure out how to make those or obtain them (likely not possible). Because of this, this tutorial is not useful.

May 2023

• 2 stars: Disliked: Instructions are insufficiently detailed (no definitions for key terms, no explanation of required file structures). The only way to use the tool is by trial and error (wastes a lot of time)

July 2022

• 2 stars: Liked: It is a useful feature. Disliked: The syntax of the "Replace text" tool is not explained. Thus, it is only useful with the data collection of the tutorial, but it does not teach how to aply it to other collections with different element identifiers. It would be great if it explained why the "Find pattern" and "Replace with" boxes are filled that way.

September 2021

• 3 stars: Liked: The short list of ways to add group tags. Disliked: How to add different group tags via workflow to members of a collection.

February 2021

• 0 stars: Liked: i like it!

April 2020

• 2 stars: Disliked: The tutorial is helpful, but more info about the different tools and adjustments made to the starting files would be helpful. Similarity info on when it is better to tag file during an analysis would also be beneficial.