Repository 'dada2_seqcounts'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts

Changeset 5:0a1224c4b781 (2021-07-02)
Previous changeset 4:d943081510da (2021-02-01) Next changeset 6:9058d8943303 (2023-06-30)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 28506788978bf5f0ce31dca09b7ca3d6d4900edb"
modified:
macros.xml
removed:
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
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diff -r d943081510da -r 0a1224c4b781 macros.xml
--- a/macros.xml Mon Feb 01 20:23:52 2021 +0000
+++ b/macros.xml Fri Jul 02 20:11:22 2021 +0000
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@@ -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">
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diff -r d943081510da -r 0a1224c4b781 tools.yml
--- a/tools.yml Mon Feb 01 20:23:52 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: []
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diff -r d943081510da -r 0a1224c4b781 topics/metagenomics/metadata.yaml
--- a/topics/metagenomics/metadata.yaml Mon Feb 01 20:23:52 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -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: ""
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diff -r d943081510da -r 0a1224c4b781 topics/metagenomics/tutorials/dada2/tutorial.bib
--- a/topics/metagenomics/tutorials/dada2/tutorial.bib Mon Feb 01 20:23:52 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -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
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diff -r d943081510da -r 0a1224c4b781 topics/metagenomics/tutorials/dada2/tutorial.md
--- a/topics/metagenomics/tutorials/dada2/tutorial.md Mon Feb 01 20:23:52 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,642 +0,0 @@\n----\n-layout: tutorial_hands_on\n-\n-title: 16S Microbial Analysis with mothur (extended)\n-zenodo_link: https://doi.org/10.5281/zenodo.800651\n-questions:\n-- What is the effect of normal variation in the gut microbiome on host health?\n-objectives:\n-- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy\n-- Using a mock community to assess the error rate of your sequencing experiment\n-- Visualize sample diversity using Krona and Phinch\n-time_estimation: \'\'\n-key_points:\n-- 16S rRNA gene sequencing analysis results depend on the many algorithms used and\n-  their settings\n-- Quality control and cleaning of your data is a crucial step in order to obtain optimal\n-  results\n-- Adding a mock community to serve as a control sample can help you asses the error\n-  rate of your experimental setup\n-- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations\n-contributors:\n-- shiltemann\n-- bebatut\n-- tnabtaf\n-\n----\n-\n-\n-# Introduction\n-{:.no_toc}\n-\n-<!-- This is a comment. -->\n-\n-General introduction about the topic and then an introduction of the\n-tutorial (the questions and the objectives). It is nice also to have a\n-scheme to sum up the pipeline used during the tutorial. The idea is to\n-give to trainees insight into the content of the tutorial and the (theoretical\n-and technical) key concepts they will learn.\n-\n-You may want to cite some publications; this can be done by adding citations to the\n-bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations\n-must be in bibtex format. If you have the DOI for the paper you wish to cite, you can\n-get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).\n-\n-With the example you will find in the `tutorial.bib` file, you can add a citation to\n-this article here in your tutorial like this:\n-{% raw %} `{% cite Batut2018 %}`{% endraw %}.\n-This will be rendered like this: {% cite Batut2018 %}, and links to a\n-[bibliography section](#bibliography) which will automatically be created at the end of the\n-tutorial.\n-\n-\n-**Please follow our\n-[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)**\n-\n-> ### Agenda\n->\n-> In this tutorial, we will cover:\n->\n-> 1. TOC\n-> {:toc}\n->\n-{: .agenda}\n-\n-# Title for your first section\n-\n-Give some background about what the trainees will be doing in the section.\n-Remember that many people reading your materials will likely be novices,\n-so make sure to explain all the relevant concepts.\n-\n-## Title for a subsection\n-Section and subsection titles will be displayed in the tutorial index on the left side of\n-the page, so try to make them informative and concise!\n-\n-# Hands-on Sections\n-Below are a series of hand-on boxes, one for each tool in your workflow file.\n-Often you may wish to combine several boxes into one or make other adjustments such\n-as breaking the tutorial into sections, we encourage you to make such changes as you\n-see fit, this is just a starting point :)\n-\n-Anywhere you find the word "***TODO***", there is something that needs to be changed\n-depending on the specifics of your tutorial.\n-\n-have fun!\n-\n-## Get data\n-\n-> ### {% icon hands_on %} Hands-on: Data upload\n->\n-> 1. Create a new history for this tutorial\n-> 2. Import the files from [Zenodo]() or from the shared data library\n->\n->    ```\n->    \n->    ```\n->    ***TODO***: *Add the files by the ones on Zenodo here (if not added)*\n->\n->    ***TODO***: *Remove the useless files (if added)*\n->\n->    {% include snippets/import_via_link.md %}\n->    {% include snippets/import_from_data_library.md %}\n->\n-> 3. Rename the datasets\n-> 4. Check that the datatype\n->\n->    {% include snippets/change_datatype.md datatype="datatypes" %}\n->\n-> 5. Add to each database a tag corresponding to ...\n->\n->    {% include snippets/add_tag.md %}\n->\n-{: .hands_on}\n-\n-# Title of the section usually corresponding to a big step in the '..b'->    {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_makeSequenceTable**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters:\n->\n->    ***TODO***: *Check parameter descriptions*\n->\n->    ***TODO***: *Consider adding a comment or tip box*\n->\n->    > ### {% icon comment %} Comment\n->    >\n->    > A comment about the tool or something else. This box can also be in the main text\n->    {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_removeBimeraDenovo**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters:\n->\n->    ***TODO***: *Check parameter descriptions*\n->\n->    ***TODO***: *Consider adding a comment or tip box*\n->\n->    > ### {% icon comment %} Comment\n->    >\n->    > A comment about the tool or something else. This box can also be in the main text\n->    {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_seqCounts**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_seqCounts** {% icon tool %} with the following parameters:\n->\n->    ***TODO***: *Check parameter descriptions*\n->\n->    ***TODO***: *Consider adding a comment or tip box*\n->\n->    > ### {% icon comment %} Comment\n->    >\n->    > A comment about the tool or something else. This box can also be in the main text\n->    {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_assignTaxonomyAddspecies**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters:\n->\n->    ***TODO***: *Check parameter descriptions*\n->\n->    ***TODO***: *Consider adding a comment or tip box*\n->\n->    > ### {% icon comment %} Comment\n->    >\n->    > A comment about the tool or something else. This box can also be in the main text\n->    {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-\n-## Re-arrange\n-\n-To create the template, each step of the workflow had its own subsection.\n-\n-***TODO***: *Re-arrange the generated subsections into sections or other subsections.\n-Consider merging some hands-on boxes to have a meaningful flow of the analyses*\n-\n-# Conclusion\n-{:.no_toc}\n-\n-Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the\n-pipeline used.\n\\ No newline at end of file\n'
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diff -r d943081510da -r 0a1224c4b781 topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga
--- a/topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga Mon Feb 01 20:23:52 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
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