# HG changeset patch # User iuc # Date 1625256645 0 # Node ID 7f3b59dee073286da94e06b414deb47bd328bf63 # Parent 04144473e59e07565adbe58271707f483db470b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 28506788978bf5f0ce31dca09b7ca3d6d4900edb" diff -r 04144473e59e -r 7f3b59dee073 macros.xml --- a/macros.xml Mon Feb 01 20:18:48 2021 +0000 +++ b/macros.xml Fri Jul 02 20:10:45 2021 +0000 @@ -7,7 +7,7 @@ - 1.18 + 1.20 0 diff -r 04144473e59e -r 7f3b59dee073 tools.yml --- a/tools.yml Mon Feb 01 20:18:48 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: [] diff -r 04144473e59e -r 7f3b59dee073 topics/metagenomics/metadata.yaml --- a/topics/metagenomics/metadata.yaml Mon Feb 01 20:18:48 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: "" diff -r 04144473e59e -r 7f3b59dee073 topics/metagenomics/tutorials/dada2/tutorial.bib --- a/topics/metagenomics/tutorials/dada2/tutorial.bib Mon Feb 01 20:18:48 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 diff -r 04144473e59e -r 7f3b59dee073 topics/metagenomics/tutorials/dada2/tutorial.md --- a/topics/metagenomics/tutorials/dada2/tutorial.md Mon Feb 01 20:18:48 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} - - - -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: - -![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* - -> ### {% 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 diff -r 04144473e59e -r 7f3b59dee073 topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga --- a/topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga Mon Feb 01 20:18:48 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": { - "batch_cond|paired_cond|reads": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "dada2: plotComplexity", - "outputs": [ - { - "name": "output_fwd", - "type": "pdf" - }, - { - "name": "output_rev", - "type": "pdf" - } - ], - "position": { - "left": 499, - "top": 178.5 - }, - "post_job_actions": { - "HideDatasetActionoutput_fwd": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_fwd" - }, - "HideDatasetActionoutput_rev": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_rev" - } - }, - "tool_id": "dada2_plotComplexity", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"kmerSize\": \"\\\"2\\\"\", \"n\": \"\\\"100000\\\"\", \"window\": \"\\\"\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"by\": \"\\\"5\\\"\", \"bins\": \"\\\"100\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "4f226c7b-9ba8-4b48-8d48-899cf345b660", - "workflow_outputs": [ - { - "label": null, - "output_name": "output_fwd", - "uuid": "52b4da66-504c-4fbe-8487-d6c0613ab6ae" - }, - { - "label": null, - "output_name": "output_rev", - "uuid": "3785a6f5-da8a-4232-b2ab-4f9f4c0732f6" - } - ] - }, - "2": { - "annotation": "", - "content_id": "dada2_plotQualityProfile", - "errors": null, - "id": 2, - "input_connections": { - "batch_cond|paired_cond|reads": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "dada2: plotQualityProfile", - "outputs": [ - { - "name": "output_fwd", - "type": "pdf" - }, - { - "name": "output_rev", - "type": "pdf" - } - ], - "position": { - "left": 496, - "top": 364 - }, - "post_job_actions": { - "HideDatasetActionoutput_fwd": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_fwd" - }, - "HideDatasetActionoutput_rev": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_rev" - } - }, - "tool_id": "dada2_plotQualityProfile", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"n\": \"\\\"500000\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"aggregate\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "f6e0a2ea-a639-48d9-ae3c-c1ec2bab93e5", - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "dada2_filterAndTrim", - "errors": null, - "id": 3, - "input_connections": { - "paired_cond|reads": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "dada2: filterAndTrim", - "outputs": [ - { - "name": "paired_output", - "type": "input" - }, - { - "name": "outtab", - "type": "tabular" - } - ], - "position": { - "left": 485, - "top": 612 - }, - "post_job_actions": { - "HideDatasetActionouttab": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outtab" - }, - "HideDatasetActionpaired_output": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "paired_output" - } - }, - "tool_id": "dada2_filterAndTrim", - "tool_state": "{\"trim\": \"{\\\"trimLeft\\\": \\\"0\\\", \\\"trimRight\\\": \\\"0\\\", \\\"truncLen\\\": \\\"0\\\", \\\"truncQ\\\": \\\"2\\\"}\", \"__page__\": null, \"rmPhiX\": \"\\\"true\\\"\", \"rmlowcomplex\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"filter\": \"{\\\"maxEE\\\": \\\"\\\", \\\"maxLen\\\": \\\"\\\", \\\"maxN\\\": \\\"0\\\", \\\"minLen\\\": \\\"20\\\", \\\"minQ\\\": \\\"0\\\"}\", \"seprev_cond\": \"{\\\"__current_case__\\\": 0, \\\"seprev_select\\\": \\\"no\\\"}\", \"output_statistics\": \"\\\"true\\\"\", \"orientFwd\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "353103fd-afc3-4fe0-a4a3-8dca75b59107", - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": "dada2_plotComplexity", - "errors": null, - "id": 4, - "input_connections": { - "batch_cond|paired_cond|reads": { - "id": 3, - "output_name": "paired_output" - } - }, - "inputs": [], - "label": null, - "name": "dada2: plotComplexity", - "outputs": [ - { - "name": "output_fwd", - "type": "pdf" - }, - { - "name": "output_rev", - "type": "pdf" - } - ], - "position": { - "left": 840, - "top": 179.5 - }, - "post_job_actions": { - "HideDatasetActionoutput_fwd": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_fwd" - }, - "HideDatasetActionoutput_rev": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_rev" - } - }, - "tool_id": "dada2_plotComplexity", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"kmerSize\": \"\\\"2\\\"\", \"n\": \"\\\"100000\\\"\", \"window\": \"\\\"\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"by\": \"\\\"5\\\"\", \"bins\": \"\\\"100\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "9c6c20be-b9d8-4645-a2d6-3ecc5bc33f4a", - "workflow_outputs": [] - }, - "5": { - "annotation": "", - "content_id": "dada2_plotQualityProfile", - "errors": null, - "id": 5, - "input_connections": { - "batch_cond|paired_cond|reads": { - "id": 3, - "output_name": "paired_output" - } - }, - "inputs": [], - "label": null, - "name": "dada2: plotQualityProfile", - "outputs": [ - { - "name": "output_fwd", - "type": "pdf" - }, - { - "name": "output_rev", - "type": "pdf" - } - ], - "position": { - "left": 842.5, - "top": 364.5 - }, - "post_job_actions": { - "HideDatasetActionoutput_fwd": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_fwd" - }, - "HideDatasetActionoutput_rev": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output_rev" - } - }, - "tool_id": "dada2_plotQualityProfile", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"n\": \"\\\"500000\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 0, \\\"aggregate\\\": \\\"true\\\", \\\"batch_select\\\": \\\"joint\\\", \\\"paired_cond\\\": {\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}}\", \"aggregate\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "b5234046-b9a9-4801-8994-496173c3ab2b", - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "__UNZIP_COLLECTION__", - "errors": null, - "id": 6, - "input_connections": { - "input": { - "id": 3, - "output_name": "paired_output" - } - }, - "inputs": [], - "label": null, - "name": "Unzip Collection", - "outputs": [ - { - "name": "forward", - "type": "input" - }, - { - "name": "reverse", - "type": "input" - } - ], - "position": { - "left": 841, - "top": 636 - }, - "post_job_actions": { - "HideDatasetActionforward": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "forward" - }, - "HideDatasetActionreverse": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "reverse" - } - }, - "tool_id": "__UNZIP_COLLECTION__", - "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", - "tool_version": "1.0.0", - "type": "tool", - "uuid": "41ab27fe-f07d-4653-b4b5-e77408957a9a", - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "dada2_learnErrors", - "errors": null, - "id": 7, - "input_connections": { - "fls": { - "id": 6, - "output_name": "forward" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool dada2: learnErrors", - "name": "fls" - } - ], - "label": null, - "name": "dada2: learnErrors", - "outputs": [ - { - "name": "errors", - "type": "dada2_errorrates" - }, - { - "name": "plot", - "type": "pdf" - } - ], - "position": { - "left": 1152, - "top": 445 - }, - "post_job_actions": { - "HideDatasetActionerrors": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "errors" - }, - "HideDatasetActionplot": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "plot" - } - }, - "tool_id": "dada2_learnErrors", - "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"err_in\\\": \\\"false\\\", \\\"err_out\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"fls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nbases\": \"\\\"8\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0.0\\\", \\\"randomize\\\": \\\"false\\\"}\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "e8c86ffd-118c-44f6-a58d-5c1704bb6ed6", - "workflow_outputs": [] - }, - "8": { - "annotation": "", - "content_id": "dada2_learnErrors", - "errors": null, - "id": 8, - "input_connections": { - "fls": { - "id": 6, - "output_name": "reverse" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool dada2: learnErrors", - "name": "fls" - } - ], - "label": null, - "name": "dada2: learnErrors", - "outputs": [ - { - "name": "errors", - "type": "dada2_errorrates" - }, - { - "name": "plot", - "type": "pdf" - } - ], - "position": { - "left": 1109, - "top": 871 - }, - "post_job_actions": { - "HideDatasetActionerrors": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "errors" - }, - "HideDatasetActionplot": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "plot" - } - }, - "tool_id": "dada2_learnErrors", - "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"err_in\\\": \\\"false\\\", \\\"err_out\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"fls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"nbases\": \"\\\"8\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0.0\\\", \\\"randomize\\\": \\\"false\\\"}\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "2cbc5056-7cc7-4e3e-a283-959a261ca4c5", - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "dada2_dada", - "errors": null, - "id": 9, - "input_connections": { - "batch_cond|derep": { - "id": 6, - "output_name": "forward" - }, - "err": { - "id": 7, - "output_name": "errors" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool dada2: dada", - "name": "batch_cond" - }, - { - "description": "runtime parameter for tool dada2: dada", - "name": "err" - } - ], - "label": null, - "name": "dada2: dada", - "outputs": [ - { - "name": "data_collection", - "type": "input" - } - ], - "position": { - "left": 1424.5, - "top": 585.5 - }, - "post_job_actions": {}, - "tool_id": "dada2_dada", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"err\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "b51bcd73-c8f0-4c39-8a23-9a5baa0a6b4f", - "workflow_outputs": [ - { - "label": null, - "output_name": "data_collection", - "uuid": "8b97daeb-3389-4140-929d-593c5d8bba3a" - } - ] - }, - "10": { - "annotation": "", - "content_id": "dada2_dada", - "errors": null, - "id": 10, - "input_connections": { - "batch_cond|derep": { - "id": 6, - "output_name": "reverse" - }, - "err": { - "id": 8, - "output_name": "errors" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool dada2: dada", - "name": "batch_cond" - }, - { - "description": "runtime parameter for tool dada2: dada", - "name": "err" - } - ], - "label": null, - "name": "dada2: dada", - "outputs": [ - { - "name": "data_collection", - "type": "input" - } - ], - "position": { - "left": 1413.5, - "top": 803.5 - }, - "post_job_actions": {}, - "tool_id": "dada2_dada", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"err\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "188c4ee7-3fb7-4dc7-8efd-30fb38c0d679", - "workflow_outputs": [ - { - "label": null, - "output_name": "data_collection", - "uuid": "7dfc0db1-2376-440c-ac0b-3f9932f063db" - } - ] - }, - "11": { - "annotation": "", - "content_id": "dada2_mergePairs", - "errors": null, - "id": 11, - "input_connections": { - "dadaF": { - "id": 9, - "output_name": "data_collection" - }, - "dadaR": { - "id": 10, - "output_name": "data_collection" - }, - "derepF": { - "id": 6, - "output_name": "forward" - }, - "derepR": { - "id": 6, - "output_name": "reverse" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool dada2: mergePairs", - "name": "dadaR" - }, - { - "description": "runtime parameter for tool dada2: mergePairs", - "name": "derepR" - }, - { - "description": "runtime parameter for tool dada2: mergePairs", - "name": "dadaF" - }, - { - "description": "runtime parameter for tool dada2: mergePairs", - "name": "derepF" - } - ], - "label": null, - "name": "dada2: mergePairs", - "outputs": [ - { - "name": "merged", - "type": "dada2_mergepairs" - } - ], - "position": { - "left": 1691, - "top": 652.5 - }, - "post_job_actions": {}, - "tool_id": "dada2_mergePairs", - "tool_state": "{\"__page__\": null, \"dadaF\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"derepR\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"maxMismatch\": \"\\\"0\\\"\", \"trimOverhang\": \"\\\"false\\\"\", \"minOverlap\": \"\\\"12\\\"\", \"justConcatenate\": \"\\\"false\\\"\", \"dadaR\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"derepF\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "8a74535a-c7a2-4c24-a907-8cb791b779bf", - "workflow_outputs": [ - { - "label": null, - "output_name": "merged", - "uuid": "887453f1-44ea-4882-8b94-91a3b02eaa0d" - } - ] - }, - "12": { - "annotation": "", - "content_id": "dada2_makeSequenceTable", - "errors": null, - "id": 12, - "input_connections": { - "samples": { - "id": 11, - "output_name": "merged" - } - }, - "inputs": [], - "label": null, - "name": "dada2: makeSequenceTable", - "outputs": [ - { - "name": "stable", - "type": "dada2_sequencetable" - }, - { - "name": "plot_output", - "type": "pdf" - } - ], - "position": { - "left": 1999, - "top": 694 - }, - "post_job_actions": { - "HideDatasetActionplot_output": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "plot_output" - }, - "HideDatasetActionstable": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "stable" - } - }, - "tool_id": "dada2_makeSequenceTable", - "tool_state": "{\"orderBy\": \"\\\"abundance\\\"\", \"plot\": \"\\\"true\\\"\", \"__page__\": null, \"filter_cond\": \"{\\\"__current_case__\\\": 0, \\\"filter_select\\\": \\\"no\\\"}\", \"samples\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "3cd64745-bb03-4bfa-b425-a16db0888967", - "workflow_outputs": [] - }, - "13": { - "annotation": "", - "content_id": "dada2_removeBimeraDenovo", - "errors": null, - "id": 13, - "input_connections": { - "unqs": { - "id": 12, - "output_name": "stable" - } - }, - "inputs": [], - "label": null, - "name": "dada2: removeBimeraDenovo", - "outputs": [ - { - "name": "stable_uniques", - "type": "dada2_uniques" - }, - { - "name": "stable_mergepairs", - "type": "dada2_mergepairs" - }, - { - "name": "stable_sequencetable", - "type": "dada2_sequencetable" - } - ], - "position": { - "left": 2299, - "top": 640 - }, - "post_job_actions": { - "HideDatasetActionstable_mergepairs": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "stable_mergepairs" - }, - "HideDatasetActionstable_sequencetable": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "stable_sequencetable" - }, - "HideDatasetActionstable_uniques": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "stable_uniques" - } - }, - "tool_id": "dada2_removeBimeraDenovo", - "tool_state": "{\"unqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"method\": \"\\\"consensus\\\"\", \"__page__\": null}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "4c001b98-d20d-4255-96ee-2b9829aa815b", - "workflow_outputs": [] - }, - "14": { - "annotation": "", - "content_id": "dada2_seqCounts", - "errors": null, - "id": 14, - "input_connections": { - "inrep_0|input": { - "id": 3, - "output_name": "outtab" - }, - "inrep_1|input": { - "id": 9, - "output_name": "data_collection" - }, - "inrep_2|input": { - "id": 10, - "output_name": "data_collection" - }, - "inrep_4|input": { - "id": 12, - "output_name": "stable" - }, - "inrep_5|input": { - "id": 13, - "output_name": "stable_sequencetable" - } - }, - "inputs": [], - "label": null, - "name": "dada2: sequence counts", - "outputs": [ - { - "name": "counts", - "type": "tabular" - } - ], - "position": { - "left": 2616, - "top": 320 - }, - "post_job_actions": { - "HideDatasetActioncounts": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "counts" - } - }, - "tool_id": "dada2_seqCounts", - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"inrep\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"filt\\\"}, {\\\"__index__\\\": 1, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised fwd\\\"}, {\\\"__index__\\\": 2, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised rev\\\"}, {\\\"__index__\\\": 3, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"merged\\\"}, {\\\"__index__\\\": 4, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"tabled\\\"}, {\\\"__index__\\\": 5, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"nochim\\\"}]\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5", - "workflow_outputs": [] - }, - "15": { - "annotation": "", - "content_id": "dada2_assignTaxonomyAddspecies", - "errors": null, - "id": 15, - "input_connections": { - "seqs": { - "id": 13, - "output_name": "stable_sequencetable" - } - }, - "inputs": [], - "label": null, - "name": "dada2: assignTaxonomy and addSpecies", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 2623, - "top": 688 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "dada2_assignTaxonomyAddspecies", - "tool_state": "{\"__page__\": null, \"tryRC\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"addSpecies_cond\": \"{\\\"__current_case__\\\": 1, \\\"addSpecies_select\\\": \\\"TRUE\\\", \\\"allowMultiple_cond\\\": {\\\"__current_case__\\\": 0, \\\"allowMultiple\\\": \\\"FALSE\\\"}, \\\"speciesreference_cond\\\": {\\\"__current_case__\\\": 0, \\\"speciesrefFasta\\\": \\\"test_buildid\\\", \\\"speciesreference_select\\\": \\\"builtin\\\"}, \\\"tryRC\\\": \\\"false\\\"}\", \"reference_cond\": \"{\\\"__current_case__\\\": 0, \\\"refFasta\\\": \\\"test_buildid\\\", \\\"reference_select\\\": \\\"builtin\\\"}\", \"outputBootstraps\": \"\\\"false\\\"\", \"minBoot\": \"\\\"50\\\"\", \"seqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.12+galaxy0", - "type": "tool", - "uuid": "babc7594-ae73-4818-919f-561836c45c17", - "workflow_outputs": [] - } - }, - "tags": [], - "uuid": "a4ba74bb-5a8a-403d-885c-822bbe9d6e03", - "version": 1 -} \ No newline at end of file