Merge pull request #4849 from Marie59/ocean_var

Update ocean variables tuto

topics/climate/tutorials/ocean-variables/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/climate/tutorials/ocean-variables/tutorial.bib

@@ -12,34 +12,7 @@
 # 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}
-}
 
 @misc{hcmrdata,
   doi = {10.13120},
@@ -51,3 +24,13 @@ @misc{hcmrdata
   year = {2022},
   copyright = {Creative Commons Attribution 4.0 International}
 }
+
+@misc{emodnet,
+  doi = {10.13120/8XM0-5M67},
+  url = {https://nodc.ogs.it/catalogs/doidetails?doi=10.13120/8xm0-5m67},
+  author = {Lipizer,  M. and Molina Jack M.,  E. and Wesslander,  K. and Fyrberg,  L. and Tsompanou,  M. and Iona,  A. and Buga,  L. and Sarbu,  G. and Gatti,  J. and Larsen M.,  M. and Giorgetti,  A.},
+  language = {en},
+  title = {EMODnet Chemistry Regional sea eutrophication data collection and Quality Control loop},
+  publisher = {OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale),  Oceanographic Section},
+  year = {2023}
+}

topics/climate/tutorials/ocean-variables/workflows/index.md

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

topics/climate/tutorials/ocean-variables/workflows/main_workflow-tests.yml

@@ -0,0 +1,7 @@
+# GTN_RUN_SKIP_REASON: Uses Interactive Tools
+- doc: Test outline for main_workflow.ga
+  job:
+    Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip:
+      class: File
+      location: https://github.com/fair-ease/Data-for-Galaxy-/raw/main/Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip
+  outputs: {}

topics/climate/tutorials/ocean-variables/workflows/main_workflow.ga

@@ -0,0 +1,165 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Subset data on the Mediterreanean see and extract and visualise the Phosphate variable",
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "0009-0008-0622-604X",
+            "name": "Marie Joss\u00e9",
+            "url": "https://github.com/Marie59"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "CC-BY-4.0",
+    "name": "Ocean's variables",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip"
+                }
+            ],
+            "label": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 2
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "04b96704-a567-4c94-8708-285fe2efb087",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "interactive_tool_odv",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "method|folder": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "ODV",
+            "outputs": [
+                {
+                    "name": "outputs_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "outputs_all",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 256,
+                "top": 16
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_odv",
+            "tool_state": "{\"__input_ext\": \"zip\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"zip\", \"__current_case__\": 1, \"folder\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.6.5.1",
+            "type": "tool",
+            "uuid": "6e83d448-87de-48da-9649-95a87a23973c",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "interactive_tool_divand",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "input": {
+                    "id": 1,
+                    "output_name": "outputs_netcdf"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Interactive DIVAnd Notebooks",
+            "outputs": [
+                {
+                    "name": "output_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "output_all",
+                    "type": "input"
+                },
+                {
+                    "name": "jupyter_notebook",
+                    "type": "ipynb"
+                }
+            ],
+            "position": {
+                "left": 515,
+                "top": 0
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_divand",
+            "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.0.5",
+            "type": "tool",
+            "uuid": "aaa2c97b-cef5-4952-b21e-b4f71a7d6e3b",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "interactive_tool_odv",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "method|infiles": {
+                    "id": 2,
+                    "output_name": "output_netcdf"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "ODV",
+            "outputs": [
+                {
+                    "name": "outputs_netcdf",
+                    "type": "input"
+                },
+                {
+                    "name": "outputs_all",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 778,
+                "top": 87
+            },
+            "post_job_actions": {},
+            "tool_id": "interactive_tool_odv",
+            "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"own_data\", \"__current_case__\": 0, \"infiles\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.6.5.1",
+            "type": "tool",
+            "uuid": "13277c72-e0e3-4353-9c2a-d3440ba1860e",
+            "when": null,
+            "workflow_outputs": []
+        }
+    },
+    "tags": [
+        "earth-system",
+        "Ocean"
+    ],
+    "uuid": "aacfc1b1-2c81-486d-8bed-5eeaef39a818",
+    "version": 2
+}