ampvis2 tutorial first upload

topics/microbiome/tutorials/visualisation-ampvis/data-library.yaml

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+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: The new topic
+  description: Summary
+  items:
+  - name: Development of statistical analysis and visualization workflows for metagenomic
+      amplicon data using the Galaxy framework
+    items:
+    - name: 'DOI: 10.5281/zenodo.11281381'
+      description: latest
+      items:
+      - url: https://zenodo.org/api/records/11281381/files/Galaxy11-[MiDAS_otushort_table.tsv].mothur.axes/content
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11281381
+      - url: https://zenodo.org/api/records/11281381/files/Galaxy1-[MiDAS_metadata.tsv].tabular/content
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11281381
+      - url: https://zenodo.org/api/records/11281381/files/Galaxy3-[MiDAS_taxtable.tsv].tabular/content
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/11281381

topics/microbiome/tutorials/visualisation-ampvis/faqs/index.md

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+---
+layout: faq-page
+---

topics/microbiome/tutorials/visualisation-ampvis/tutorial.bib

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+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Batut2018,
+  doi = {10.1016/j.cels.2018.05.012},
+  url = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year = {2018},
+  month = jun,
+  publisher = {Elsevier {BV}},
+  volume = {6},
+  number = {6},
+  pages = {752--758.e1},
+  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
+           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
+           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
+           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
+           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
+           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}

topics/microbiome/tutorials/visualisation-ampvis/tutorial.md

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+---
+layout: tutorial_hands_on
+
+title: Development of statistical analysis and visualization workflows for metagenomic
+  amplicon data using the Galaxy framework
+level: Intermediate
+zenodo_link: https://zenodo.org/records/11281381
+questions:
+- If we generated amplicon data, how can we analyse it with Galaxy ampvis2 tools?
+- How can we visualise amplicon data by using heatmap, ordination plot, boxplot, rarefraction curve or timeseries?
+objectives:
+- use heatmap workflow to analyse and visualise amplicon data
+- or use ordination plot, or boxplot, or rarefraction curve, or timeseries
+- use grouped data or grouped data with facets
+time_estimation: 3H
+key_points:
+- using different visualisation methods can present data from other points of view
+- with enough metadata the data can be visualised w.r.t. groups and facets 
+contributors:
+- lenaarenot
+- contributor2
+
+---
+
+
+
+General introduction about the topic and then an introduction of the
+tutorial (the questions and the objectives). It is nice also to have a
+scheme to sum up the pipeline used during the tutorial. The idea is to
+give to trainees insight into the content of the tutorial and the (theoretical
+and technical) key concepts they will learn.
+
+You may want to cite some publications; this can be done by adding citations to the
+bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations
+must be in bibtex format. If you have the DOI for the paper you wish to cite, you can
+get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).
+
+With the example you will find in the `tutorial.bib` file, you can add a citation to
+this article here in your tutorial like this:
+{% raw %} `{% cite Batut2018 %}`{% endraw %}.
+This will be rendered like this: {% cite Batut2018 %}, and links to a
+[bibliography section](#bibliography) which will automatically be created at the end of the
+tutorial.
+
+<!-- This is a comment. -->
+
+**Please follow our
+[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)**
+
+> <agenda-title></agenda-title>
+>
+> In this tutorial, we will cover:
+>
+> 1. TOC
+> {:toc}
+>
+{: .agenda}
+
+# Title for your first section
+
+Give some background about what the trainees will be doing in the section.
+Remember that many people reading your materials will likely be novices,
+so make sure to explain all the relevant concepts.
+
+## Title for a subsection
+Section and subsection titles will be displayed in the tutorial index on the left side of
+the page, so try to make them informative and concise!
+
+# Hands-on Sections
+Below are a series of hand-on boxes, one for each tool in your workflow file.
+Often you may wish to combine several boxes into one or make other adjustments such
+as breaking the tutorial into sections, we encourage you to make such changes as you
+see fit, this is just a starting point :)
+
+Anywhere you find the word "***TODO***", there is something that needs to be changed
+depending on the specifics of your tutorial.
+
+have fun!
+
+## Get data
+
+> <hands-on-title> Data Upload </hands-on-title>
+>
+> 1. Create a new history for this tutorial
+> 2. Import the files from [Zenodo]({{ page.zenodo_link }}) or from
+>    the shared data library (`GTN - Material` -> `{{ page.topic_name }}`
+>     -> `{{ page.title }}`):
+>
+>    ```
+>    https://zenodo.org/api/records/11281381/files/Galaxy11-[MiDAS_otushort_table.tsv].mothur.axes/content
+>    https://zenodo.org/api/records/11281381/files/Galaxy1-[MiDAS_metadata.tsv].tabular/content
+>    https://zenodo.org/api/records/11281381/files/Galaxy3-[MiDAS_taxtable.tsv].tabular/content
+>    ```
+>    ***TODO***: *Add the files by the ones on Zenodo here (if not added)*
+>
+>    ***TODO***: *Remove the useless files (if added)*
+>
+>    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
+>    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
+>
+> 3. Rename the datasets
+> 4. Check that the datatype
+>
+>    {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %}
+>
+> 5. Add to each database a tag corresponding to ...
+>
+>    {% snippet faqs/galaxy/datasets_add_tag.md %}
+>
+{: .hands_on}
+
+# Title of the section usually corresponding to a big step in the analysis
+
+It comes first a description of the step: some background and some theory.
+Some image can be added there to support the theory explanation:
+
+![Alternative text](../../images/image_name "Legend of the image")
+
+The idea is to keep the theory description before quite simple to focus more on the practical part.
+
+***TODO***: *Consider adding a detail box to expand the theory*
+
+> <details-title> More details about the theory </details-title>
+>
+> But to describe more details, it is possible to use the detail boxes which are expandable
+>
+{: .details}
+
+A big step can have several subsections or sub steps:
+
+
+## Sub-step with **ampvis2 load**
+
+> <hands-on-title> Task description </hands-on-title>
+>
+> 1. {% tool [ampvis2 load](toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.6+galaxy1) %} with the following parameters:
+>    - {% icon param-file %} *"OTU table"*: `output` (Input dataset)
+>    - {% icon param-file %} *"Sample metadata"*: `output` (Input dataset)
+>    - {% icon param-file %} *"Taxonomy table"*: `output` (Input dataset)
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> <question-title></question-title>
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > <solution-title></solution-title>
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **ampvis2 subset samples**
+
+> <hands-on-title> Task description </hands-on-title>
+>
+> 1. {% tool [ampvis2 subset samples](toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_subset_samples/ampvis2_subset_samples/2.8.6+galaxy1) %} with the following parameters:
+>    - {% icon param-file %} *"Ampvis2 RDS dataset"*: `ampvis` (output of **ampvis2 load** {% icon tool %})
+>    - {% icon param-file %} *"Metadata list"*: `metadata_list_out` (output of **ampvis2 load** {% icon tool %})
+>    - *"Metadata variable"*: ``
+>    - *"Metadata value(s)"*: ``
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> <question-title></question-title>
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > <solution-title></solution-title>
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **ampvis2 heatmap**
+
+> <hands-on-title> Task description </hands-on-title>
+>
+> 1. {% tool [ampvis2 heatmap](toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_heatmap/ampvis2_heatmap/2.8.6+galaxy1) %} with the following parameters:
+>    - {% icon param-file %} *"Ampvis2 RDS dataset"*: `ampvis` (output of **ampvis2 subset samples** {% icon tool %})
+>    - {% icon param-file %} *"Metadata list"*: `metadata_list_out` (output of **ampvis2 subset samples** {% icon tool %})
+>    - *"Group samples"*: ``
+>    - *"Facet the samples"*: ``
+>    - *"The taxonomic level to aggregate the OTUs"*: `Species`
+>    - *"Additional taxonomic level(s) to display"*: ``
+>    - *"Limit the number of shown taxa"*: `Select a number of taxa to show`
+>    - *"Plot the values on the heatmap"*: `Yes`
+>    - *"Sort heatmap by most abundant taxa"*: `No`
+>    - *"Show functional information about the Genus-level OTUs"*: `No`
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > <comment-title> short description </comment-title>
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> <question-title></question-title>
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > <solution-title></solution-title>
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+
+## Re-arrange
+
+To create the template, each step of the workflow had its own subsection.
+
+***TODO***: *Re-arrange the generated subsections into sections or other subsections.
+Consider merging some hands-on boxes to have a meaningful flow of the analyses*
+
+# Conclusion
+
+Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the
+pipeline used.

topics/microbiome/tutorials/visualisation-ampvis/workflows/index.md

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+---
+layout: workflow-list
+---