| Previous changeset 4:8c202e741d68 (2021-02-01) Next changeset 6:0776d824d896 (2023-06-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 28506788978bf5f0ce31dca09b7ca3d6d4900edb" |
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modified:
macros.xml |
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removed:
tools.yml topics/metagenomics/metadata.yaml topics/metagenomics/tutorials/dada2/tutorial.bib topics/metagenomics/tutorials/dada2/tutorial.md topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga |
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| diff -r 8c202e741d68 -r 04c15826a0b8 macros.xml --- a/macros.xml Mon Feb 01 20:13:14 2021 +0000 +++ b/macros.xml Fri Jul 02 20:13:11 2021 +0000 |
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| @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@DADA2_VERSION@">1.18</token> + <token name="@DADA2_VERSION@">1.20</token> <token name="@WRAPPER_VERSION@">0</token> <xml name="version_command"> |
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| diff -r 8c202e741d68 -r 04c15826a0b8 tools.yml --- a/tools.yml Mon Feb 01 20:13:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -install_tool_dependencies: True -install_repository_dependencies: True -install_resolver_dependencies: True - -tools: [] |
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| diff -r 8c202e741d68 -r 04c15826a0b8 topics/metagenomics/metadata.yaml --- a/topics/metagenomics/metadata.yaml Mon Feb 01 20:13:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,28 +0,0 @@ ---- -name: "metagenomics" -type: "use" -title: "Metagenomics" -summary: "Metagenomics is a discipline that enables the genomic study of uncultured microorganisms" -edam_ontology: "topic_3174" -docker_image: "quay.io/galaxy/metagenomics-training" - -requirements: - - - type: "internal" - topic_name: introduction - -maintainers: - - bebatut - - shiltemann - -references: - - - authors: "Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD." - title: "Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology" - link: "http://www.schlosslab.org/assets/pdf/2013_kozich.pdf" - summary: "" - - - authors: "Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra" - title: "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences." - link: "https://www.ncbi.nlm.nih.gov/pubmed/25118885" - summary: "" |
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| diff -r 8c202e741d68 -r 04c15826a0b8 topics/metagenomics/tutorials/dada2/tutorial.bib --- a/topics/metagenomics/tutorials/dada2/tutorial.bib Mon Feb 01 20:13:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,30 +0,0 @@ - -# This is the bibliography file for your tutorial. -# -# To add bibliography (bibtex) entries here, follow these steps: -# 1) Find the DOI for the article you want to cite -# 2) Go to https://doi2bib.org and fill in the DOI -# 3) Copy the resulting bibtex entry into this file -# -# To cite the example below, in your tutorial.md file -# use {% Batut2018 %} - -@article{Batut2018, - doi = {10.1016/j.cels.2018.05.012}, - url = {https://doi.org/10.1016/j.cels.2018.05.012}, - year = {2018}, - month = jun, - publisher = {Elsevier {BV}}, - volume = {6}, - number = {6}, - pages = {752--758.e1}, - author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and - Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton - and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and - Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and - Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and - Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and - Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning}, - title = {Community-Driven Data Analysis Training for Biology}, - journal = {Cell Systems} -} \ No newline at end of file |
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| diff -r 8c202e741d68 -r 04c15826a0b8 topics/metagenomics/tutorials/dada2/tutorial.md --- a/topics/metagenomics/tutorials/dada2/tutorial.md Mon Feb 01 20:13:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,642 +0,0 @@\n----\n-layout: tutorial_hands_on\n-\n-title: 16S Microbial Analysis with mothur (extended)\n-zenodo_link: https://doi.org/10.5281/zenodo.800651\n-questions:\n-- What is the effect of normal variation in the gut microbiome on host health?\n-objectives:\n-- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy\n-- Using a mock community to assess the error rate of your sequencing experiment\n-- Visualize sample diversity using Krona and Phinch\n-time_estimation: \'\'\n-key_points:\n-- 16S rRNA gene sequencing analysis results depend on the many algorithms used and\n- their settings\n-- Quality control and cleaning of your data is a crucial step in order to obtain optimal\n- results\n-- Adding a mock community to serve as a control sample can help you asses the error\n- rate of your experimental setup\n-- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations\n-contributors:\n-- shiltemann\n-- bebatut\n-- tnabtaf\n-\n----\n-\n-\n-# Introduction\n-{:.no_toc}\n-\n-<!-- This is a comment. -->\n-\n-General introduction about the topic and then an introduction of the\n-tutorial (the questions and the objectives). It is nice also to have a\n-scheme to sum up the pipeline used during the tutorial. The idea is to\n-give to trainees insight into the content of the tutorial and the (theoretical\n-and technical) key concepts they will learn.\n-\n-You may want to cite some publications; this can be done by adding citations to the\n-bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations\n-must be in bibtex format. If you have the DOI for the paper you wish to cite, you can\n-get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).\n-\n-With the example you will find in the `tutorial.bib` file, you can add a citation to\n-this article here in your tutorial like this:\n-{% raw %} `{% cite Batut2018 %}`{% endraw %}.\n-This will be rendered like this: {% cite Batut2018 %}, and links to a\n-[bibliography section](#bibliography) which will automatically be created at the end of the\n-tutorial.\n-\n-\n-**Please follow our\n-[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)**\n-\n-> ### Agenda\n->\n-> In this tutorial, we will cover:\n->\n-> 1. TOC\n-> {:toc}\n->\n-{: .agenda}\n-\n-# Title for your first section\n-\n-Give some background about what the trainees will be doing in the section.\n-Remember that many people reading your materials will likely be novices,\n-so make sure to explain all the relevant concepts.\n-\n-## Title for a subsection\n-Section and subsection titles will be displayed in the tutorial index on the left side of\n-the page, so try to make them informative and concise!\n-\n-# Hands-on Sections\n-Below are a series of hand-on boxes, one for each tool in your workflow file.\n-Often you may wish to combine several boxes into one or make other adjustments such\n-as breaking the tutorial into sections, we encourage you to make such changes as you\n-see fit, this is just a starting point :)\n-\n-Anywhere you find the word "***TODO***", there is something that needs to be changed\n-depending on the specifics of your tutorial.\n-\n-have fun!\n-\n-## Get data\n-\n-> ### {% icon hands_on %} Hands-on: Data upload\n->\n-> 1. Create a new history for this tutorial\n-> 2. Import the files from [Zenodo]() or from the shared data library\n->\n-> ```\n-> \n-> ```\n-> ***TODO***: *Add the files by the ones on Zenodo here (if not added)*\n->\n-> ***TODO***: *Remove the useless files (if added)*\n->\n-> {% include snippets/import_via_link.md %}\n-> {% include snippets/import_from_data_library.md %}\n->\n-> 3. Rename the datasets\n-> 4. Check that the datatype\n->\n-> {% include snippets/change_datatype.md datatype="datatypes" %}\n->\n-> 5. Add to each database a tag corresponding to ...\n->\n-> {% include snippets/add_tag.md %}\n->\n-{: .hands_on}\n-\n-# Title of the section usually corresponding to a big step in the '..b'-> {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_makeSequenceTable**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters:\n->\n-> ***TODO***: *Check parameter descriptions*\n->\n-> ***TODO***: *Consider adding a comment or tip box*\n->\n-> > ### {% icon comment %} Comment\n-> >\n-> > A comment about the tool or something else. This box can also be in the main text\n-> {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_removeBimeraDenovo**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters:\n->\n-> ***TODO***: *Check parameter descriptions*\n->\n-> ***TODO***: *Consider adding a comment or tip box*\n->\n-> > ### {% icon comment %} Comment\n-> >\n-> > A comment about the tool or something else. This box can also be in the main text\n-> {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_seqCounts**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_seqCounts** {% icon tool %} with the following parameters:\n->\n-> ***TODO***: *Check parameter descriptions*\n->\n-> ***TODO***: *Consider adding a comment or tip box*\n->\n-> > ### {% icon comment %} Comment\n-> >\n-> > A comment about the tool or something else. This box can also be in the main text\n-> {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-## Sub-step with **dada2_assignTaxonomyAddspecies**\n-\n-> ### {% icon hands_on %} Hands-on: Task description\n->\n-> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters:\n->\n-> ***TODO***: *Check parameter descriptions*\n->\n-> ***TODO***: *Consider adding a comment or tip box*\n->\n-> > ### {% icon comment %} Comment\n-> >\n-> > A comment about the tool or something else. This box can also be in the main text\n-> {: .comment}\n->\n-{: .hands_on}\n-\n-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*\n-\n-> ### {% icon question %} Questions\n->\n-> 1. Question1?\n-> 2. Question2?\n->\n-> > ### {% icon solution %} Solution\n-> >\n-> > 1. Answer for question1\n-> > 2. Answer for question2\n-> >\n-> {: .solution}\n->\n-{: .question}\n-\n-\n-## Re-arrange\n-\n-To create the template, each step of the workflow had its own subsection.\n-\n-***TODO***: *Re-arrange the generated subsections into sections or other subsections.\n-Consider merging some hands-on boxes to have a meaningful flow of the analyses*\n-\n-# Conclusion\n-{:.no_toc}\n-\n-Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the\n-pipeline used.\n\\ No newline at end of file\n' |
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| diff -r 8c202e741d68 -r 04c15826a0b8 topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga --- a/topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga Mon Feb 01 20:13:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,798 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "dada2 for paired data (imported from uploaded file)", \n- "steps": {\n- "0": {\n- "annotation": "", \n- "content_id": null, \n- "errors": null, \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "", \n- "name": "Input Dataset Collection"\n- }\n- ], \n- "label": null, \n- "name": "Input dataset collection", \n- "outputs": [], \n- "position": {\n- "left": 200, \n- "top": 613\n- }, \n- "tool_id": null, \n- "tool_state": "{\\"collection_type\\": \\"list:paired\\", \\"name\\": \\"Input Dataset Collection\\"}", \n- "tool_version": null, \n- "type": "data_collection_input", \n- "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f", \n- "workflow_outputs": []\n- }, \n- "1": {\n- "annotation": "", \n- "content_id": "dada2_plotComplexity", \n- "errors": null, \n- "id": 1, \n- "input_connections": {\n- "batch_cond|paired_cond|reads": {\n- "id": 0, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "dada2: plotComplexity", \n- "outputs": [\n- {\n- "name": "output_fwd", \n- "type": "pdf"\n- }, \n- {\n- "name": "output_rev", \n- "type": "pdf"\n- }\n- ], \n- "position": {\n- "left": 499, \n- "top": 178.5\n- }, \n- "post_job_actions": {\n- "HideDatasetActionoutput_fwd": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "output_fwd"\n- }, \n- "HideDatasetActionoutput_rev": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "output_rev"\n- }\n- }, \n- "tool_id": "dada2_plotComplexity", \n- "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\\\\\\"\\"}", \n- "tool_version": "1.12+galaxy0", \n- "type": "tool", \n- "uuid": "4f226c7b-9ba8-4b48-8d48-899cf345b660", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output_fwd", \n- "uuid": "52b4da66-504c-4fbe-8487-d6c0613ab6ae"\n- }, \n- {\n- "label": null, \n- "output_name": "output_rev", \n- "uuid": "3785a6f5-da8a-4232-b2ab-4f9f4c0732f6"\n- }\n- ]\n- }, \n- "2": {\n- "annotation": "", \n- "content_id": "dada2_plotQualityProfile", \n- "errors": null, \n- "id": 2, \n- "input_connections": {\n- "batch_cond|paired_cond|reads": {\n- "id": 0, \n- "output_name": "output"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "dada2'..b' }, \n- "inputs": [], \n- "label": null, \n- "name": "dada2: sequence counts", \n- "outputs": [\n- {\n- "name": "counts", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 2616, \n- "top": 320\n- }, \n- "post_job_actions": {\n- "HideDatasetActioncounts": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "counts"\n- }\n- }, \n- "tool_id": "dada2_seqCounts", \n- "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\\\\\\"\\"}", \n- "tool_version": "1.12+galaxy0", \n- "type": "tool", \n- "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5", \n- "workflow_outputs": []\n- }, \n- "15": {\n- "annotation": "", \n- "content_id": "dada2_assignTaxonomyAddspecies", \n- "errors": null, \n- "id": 15, \n- "input_connections": {\n- "seqs": {\n- "id": 13, \n- "output_name": "stable_sequencetable"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "dada2: assignTaxonomy and addSpecies", \n- "outputs": [\n- {\n- "name": "output", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 2623, \n- "top": 688\n- }, \n- "post_job_actions": {\n- "HideDatasetActionoutput": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "output"\n- }\n- }, \n- "tool_id": "dada2_assignTaxonomyAddspecies", \n- "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\\\\\\"\\"}", \n- "tool_version": "1.12+galaxy0", \n- "type": "tool", \n- "uuid": "babc7594-ae73-4818-919f-561836c45c17", \n- "workflow_outputs": []\n- }\n- }, \n- "tags": [], \n- "uuid": "a4ba74bb-5a8a-403d-885c-822bbe9d6e03", \n- "version": 1\n-}\n\\ No newline at end of file\n' |