Mercurial > repos > iuc > dada2_mergepairs
changeset 5:1d75bd0595e2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 28506788978bf5f0ce31dca09b7ca3d6d4900edb"
| author | iuc |
|---|---|
| date | Fri, 02 Jul 2021 20:10:11 +0000 |
| parents | 306a40d4bb8f |
| children | 84743da21318 |
| files | macros.xml tools.yml topics/metagenomics/metadata.yaml topics/metagenomics/tutorials/dada2/tutorial.bib topics/metagenomics/tutorials/dada2/tutorial.md topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga |
| diffstat | 6 files changed, 1 insertions(+), 1504 deletions(-) [+] |
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--- a/macros.xml Mon Feb 01 20:22:27 2021 +0000 +++ b/macros.xml Fri Jul 02 20:10:11 2021 +0000 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@DADA2_VERSION@">1.18</token> + <token name="@DADA2_VERSION@">1.20</token> <token name="@WRAPPER_VERSION@">0</token> <xml name="version_command">
--- a/tools.yml Mon Feb 01 20:22:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -install_tool_dependencies: True -install_repository_dependencies: True -install_resolver_dependencies: True - -tools: []
--- a/topics/metagenomics/metadata.yaml Mon Feb 01 20:22:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ ---- -name: "metagenomics" -type: "use" -title: "Metagenomics" -summary: "Metagenomics is a discipline that enables the genomic study of uncultured microorganisms" -edam_ontology: "topic_3174" -docker_image: "quay.io/galaxy/metagenomics-training" - -requirements: - - - type: "internal" - topic_name: introduction - -maintainers: - - bebatut - - shiltemann - -references: - - - authors: "Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD." - title: "Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology" - link: "http://www.schlosslab.org/assets/pdf/2013_kozich.pdf" - summary: "" - - - authors: "Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra" - title: "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences." - link: "https://www.ncbi.nlm.nih.gov/pubmed/25118885" - summary: ""
--- a/topics/metagenomics/tutorials/dada2/tutorial.bib Mon Feb 01 20:22:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - -# 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 {% Batut2018 %} - -@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} -} \ No newline at end of file
--- a/topics/metagenomics/tutorials/dada2/tutorial.md Mon Feb 01 20:22:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,642 +0,0 @@ ---- -layout: tutorial_hands_on - -title: 16S Microbial Analysis with mothur (extended) -zenodo_link: https://doi.org/10.5281/zenodo.800651 -questions: -- What is the effect of normal variation in the gut microbiome on host health? -objectives: -- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy -- Using a mock community to assess the error rate of your sequencing experiment -- Visualize sample diversity using Krona and Phinch -time_estimation: '' -key_points: -- 16S rRNA gene sequencing analysis results depend on the many algorithms used and - their settings -- Quality control and cleaning of your data is a crucial step in order to obtain optimal - results -- Adding a mock community to serve as a control sample can help you asses the error - rate of your experimental setup -- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations -contributors: -- shiltemann -- bebatut -- tnabtaf - ---- - - -# Introduction -{:.no_toc} - -<!-- This is a comment. --> - -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. - - -**Please follow our -[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)** - -> ### Agenda -> -> 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 - -> ### {% icon hands_on %} Hands-on: Data upload -> -> 1. Create a new history for this tutorial -> 2. Import the files from [Zenodo]() or from the shared data library -> -> ``` -> -> ``` -> ***TODO***: *Add the files by the ones on Zenodo here (if not added)* -> -> ***TODO***: *Remove the useless files (if added)* -> -> {% include snippets/import_via_link.md %} -> {% include snippets/import_from_data_library.md %} -> -> 3. Rename the datasets -> 4. Check that the datatype -> -> {% include snippets/change_datatype.md datatype="datatypes" %} -> -> 5. Add to each database a tag corresponding to ... -> -> {% include snippets/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: - - - -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* - -> ### {% icon details %} More details about the theory -> -> 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 **dada2_plotComplexity** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_plotQualityProfile** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_filterAndTrim** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_filterAndTrim** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_plotComplexity** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_plotQualityProfile** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **Unzip Collection** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **Unzip Collection** {% icon tool %} with the following parameters: -> - {% icon param-file %} *"Input Paired Dataset"*: `paired_output` (output of **dada2_filterAndTrim** {% icon tool %}) -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_learnErrors** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_learnErrors** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_learnErrors** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_learnErrors** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_dada** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_dada** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_dada** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_dada** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_mergePairs** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_mergePairs** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_makeSequenceTable** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_removeBimeraDenovo** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_seqCounts** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_seqCounts** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 1. Answer for question1 -> > 2. Answer for question2 -> > -> {: .solution} -> -{: .question} - -## Sub-step with **dada2_assignTaxonomyAddspecies** - -> ### {% icon hands_on %} Hands-on: Task description -> -> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters: -> -> ***TODO***: *Check parameter descriptions* -> -> ***TODO***: *Consider adding a comment or tip box* -> -> > ### {% icon comment %} Comment -> > -> > 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* - -> ### {% icon question %} Questions -> -> 1. Question1? -> 2. Question2? -> -> > ### {% icon solution %} Solution -> > -> > 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 -{:.no_toc} - -Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the -pipeline used. \ No newline at end of file
--- a/topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga Mon Feb 01 20:22:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,798 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "dada2 for paired data (imported from uploaded file)", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Input Dataset Collection" - } - ], - "label": null, - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 200, - "top": 613 - }, - "tool_id": null, - "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f", - "workflow_outputs": [] - }, - "1": { - "annotation": "", - "content_id": "dada2_plotComplexity", - "errors": null, - "id": 1, - "input_connections": { - 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