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(-) [+]
line wrap: on
line diff
--- 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:
-
-![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
--- 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": {
-                "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