Add a tutorial for MetaShRIMPS

topics/ecology/tutorials/Metashrimps_tutorial/data-library.yaml

@@ -0,0 +1,13 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: New topic
+  description: Topic summary
+  items:
+  - name: Creating Quality FAIR assessment reports and draft of Data Papers from EML
+      metadata with MetaShRIMPS
+    items: []

topics/ecology/tutorials/Metashrimps_tutorial/faqs/import_files.md

@@ -0,0 +1,11 @@
+---
+title: Import files
+description: Import the files from Zenodo
+area: datasets
+box_type: tip
+layout: faq
+contributors: [TanguyGen]
+---
+
+* Click on the copy on the top right of the black zone that will appear when you will hover the cursor there to copy the link
+* Open a new navigator page and paste with **Ctrl - V** or by **right click- paste** in search bar situated at the top of the page to save the file in your computer

topics/ecology/tutorials/Metashrimps_tutorial/tutorial.bib

@@ -0,0 +1,42 @@
+
+# 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 {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@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}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}

topics/ecology/tutorials/Metashrimps_tutorial/tutorial.md

@@ -0,0 +1,134 @@
+---
+layout: tutorial_hands_on
+
+title: Creating FAIR Quality assessment reports and draft of Data Papers from EML
+  metadata with MetaShRIMPS
+zenodo_link: https://doi.org/10.5281/zenodo.8130567
+questions:
+- How to improve the FAIR quality of an EML metadata ?
+- How to use metadata for machine actionnable processes ?
+- What is the point of having a FAIR metadata ?
+objectives:
+- Learn how to use the interactive tool Metashrimps
+- Understand the challenges MetaShRIMPS is trying to respond to
+- Learn how to create a FAIR Quality assessment report from a metadata using EML standard
+- Understand the concept of Data Paper and learn how to produce it
+- Explain the necessity of using such tools when producing ecological metadata
+time_estimation: 30mn
+key_points:
+- This tool aims to improve FAIR quality of metadata
+- Creating metadata as FAIR as possible is a must
+- Be carefull of the format and standard of metadata used only EML metadata will work
+tags:
+  - Metadata
+  - EML
+  - FAIR
+  - Data Paper
+contributors:
+- TanguyGen
+- yvanlebras
+
+---
+
+
+# Introduction
+
+This tutorial aims to teach how to use the interactive tool MetaShRIMPS, available on Galaxy Ecology,
+to produce Data Papers drafts and FAIR quality assessment reports from metadata using EML
+standard.
+This tutorial purpose is also to explain why it is needed to improve the overall FAIR quality
+of metadata and how this tool responds to this necessity.
+
+> <comment-title>What does FAIR mean?</comment-title>
+> [FAIR](https://www.go-fair.org/fair-principles/) stand for **Findable, Accessible, Interoperable, Reusable**. 
+>
+>
+><img src="./Images/FAIR_data_principles.jpg" alt="FAIR Data Principles" width="500"/>
+
+>These principles were [officialy instaured in 2016](https://doi.org/10.1038/sdata.2016.18) to improve the access and usabiliy of data by the machine and to help making data reusable and shareable for users.
+>Metadata is the data used to describe and explain all the context behind the production of data. It is necessary to produce a rich and FAIR metadata in order 
+>to permit external users to understand and reuse data for their own studies.
+{:  .comment}
+> <agenda-title></agenda-title>
+>
+> In this tutorial, we will cover:
+>
+> 1. TOC
+> {:toc}
+>
+{: .agenda}
+
+
+# How can this tool improve the metadata quality?
+
+The purpose of this tool is to help the user improve their metadata quality in order to increase its value to the scientific community and to help highlighting
+the work of all the producers of the data.
+To respond to this objective, this tool aims to give an easy access to a quality assessment report of EML metadata which could guide the producers of
+data/metadata to the production of a metadata with high degree of FAIRness.
+The other objective of this tool is to highlight the work of all of the people that helped in producing this data by giving the access of a draft of Data Paper
+that is reuseable either in a non editable HTML file, that can represent the metadata in a more ergonomic way facilitating its understanding and shareability,
+or in an editable docx file. Having an editable Data Paper draft will allow the producer to complete/modify the draft of Data Paper so that it could become
+publishable as a real Data Paper giving recognition to all the people that helped producing the data.
+
+> <comment-title>What is a Data Paper?</comment-title>
+> According to the [GBIF](https://www.gbif.org/data-papers) (Global Biodiversity Information Facility), 
+>A data paper is a peer reviewed document describing a dataset, published in a peer reviewed journal. It takes effort to prepare, curate and describe data. 
+>Data papers provide recognition for this effort by means of a scholarly article.
+{:  .comment}
+# Get data
+
+> <hands-on-title> Data Upload </hands-on-title>
+>
+> 1. Create a new history for this tutorial
+> 2.Import this metadata file from [Zenodo]({{ https://doi.org/10.5281/zenodo.8130567 }}) to test it
+>     -> `{{ Training Data for "Creating Quality FAIR assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS" }}`):
+>    ```
+>    https://zenodo.org/record/8130567/files/Kakila_database_marine_mammal.xml
+>    ```
+>
+>    {% snippet topics/ecology/tutorials/Metashrimps_tutorial/import_files.md %}
+
+# Upload Data in MetaShRIMPS
+
+When oppening MetaShRIMPS, you will have an interface looking like this :
+
+<img src="./Images/upload_1.png" alt="FAIR Data Principles" width="500"/>
+
+To upload data on MetaShRIMPS, if you was selecting the xml file as input of the tool, it is already launched, if not, you have to click on the browse button and select in your local folders, the file
+you want to use. 
+> <warning-title>Select the right format</warning-title>
+> The file uploaded in this tool must be a metadata in XML format using EML metadata standard.
+{: .warning}
+
+<img src="./Images/upload_2.png" alt="FAIR Data Principles" width="500"/>
+
+After uploading the file, or if you have indicate it as input data if the tool, you just have to click on **Execute** to launch the tool with the file.
+
+# Outputs
+
+After clicking the **Execute** button, 2 new tabs called "Draft of Data Paper" and "Fair Assessment"  will appear.
+You can access all of the tool outputs by clicking on each tab (it can take a little time for your results to be displayed).
+
+## Draft of Data Paper
+
+By clicking on the "Draft of Data Paper" tab, you will have access to the draft of Data Paper presented in an HTML format.
+You can either navigate through the Data Paper with the tabs or with the scrollbar on the right and access different elements.
+
+You can at the top of the page download the draft in either an HTML format or an editable docx format.
+![Download in HTML](./Images/Download_HTML.png""Download in HTML")![Download in docx](./Images/Download_docx.png "Download in docx*)
+
+## Fair Quality Assessment report
+
+By clicking on the "Fair Assessment" tab, you will access the FAIR Quality report of the metadata uploaded.
+You will have access to different figures such as a table displaying the results of all checks tested for your metadata.
+![Table of results](./Images/Fairscore_tab.png "Example of the table displaying the results of the Quality Checks")
+
+You will also have acces to a graph presenting scores of Quality for each of the FAIR principles tested (Findable,
+Acessible, Interoperable, Reusable) on a 100 point scale.
+
+![FAIR scores](./Images/Fairscore_bar.png "Example of a FAIR score")
+
+# Conclusion
+
+Here is the end of this short tutorial aiming in explaining the purpose of MetaShRIMPS and how to use it.
+Don't hesitate to contact us if you have any questions :)

topics/ecology/tutorials/Metashrimps_tutorial/workflows/index.md

@@ -0,0 +1,3 @@
+---
+layout: workflow-list
+---

topics/ecology/tutorials/Metashrimps_tutorial/workflows/main_workflow.ga

@@ -0,0 +1 @@
+{"a_galaxy_workflow": "true", "annotation": "", "creator": [{"class": "Person", "name": "Genthon, Tanguy"}], "format-version": "0.1", "license": "CC-BY-4.0", "name": "Metashrimps", "steps": {"0": {"annotation": "", "content_id": "interactive_tool_metashrimps", "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "runtime parameter for tool metashrimps", "name": "infile"}], "label": null, "name": "metashrimps", "outputs": [{"name": "outfile", "type": "txt"}], "position": {"left": 0, "top": 0}, "post_job_actions": {}, "tool_id": "interactive_tool_metashrimps", "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.1", "type": "tool", "uuid": "c8365f00-d95b-48f3-9d50-4f743496d992", "when": null, "workflow_outputs": []}}, "tags": ["Metadata", "FAIR", "Data", "Paper"], "uuid": "5006662f-5725-4889-aa49-bc190ecdd487", "version": 2}