Merge pull request #4682 from PaulineSGN/PaulineSGN-patch-1

Add Ecoregionalization_tutorial

CONTRIBUTORS.yaml

@@ -1829,6 +1829,12 @@ paulineauffret:
     name: Pauline Auffret
     joined: 2022-08
 
+PaulineSGN:
+    name: Pauline Seguineau
+    joined: 2024-01
+    email: [email protected]
+    orcid: 0009-0009-5969-8478
+
 pauldg:
     name: Paul De Geest
     joined: 2023-04
@@ -1940,6 +1946,12 @@ rahmot:
     joined: 2021-10
     linkedin: rahmot-afolabi
 
+Rassine:
+    name: Ankerl Yassine
+    email: [email protected]
+    orcid: 0009-0007-1538-2303
+    joined: 2024-07
+
 r1corre:
     name: Erwan Corre
     email: [email protected]

topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.bib

@@ -0,0 +1,79 @@
+
+# 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{Hemery2011, 
+  doi={10.3354/meps09330}, 
+  url={http://dx.doi.org/10.3354/meps09330},
+  year={2011},
+  month=nov,
+  publisher={Inter-Research Science Center}, 
+  volume={441},
+  pages={105–116}, 
+  author={Hemery, LG and Galton-Fenzi, B and Améziane, N and Riddle, MJ and Rintoul, SR and Beaman, RJ and Post, AL and Eléaume, M}, 
+  title={Predicting habitat preferences for Anthometrina adriani (Echinodermata) on the East Antarctic continental shelf}, 
+  journal={Marine Ecology Progress Series}, 
+  ISSN={1616-1599} 
+}
+
+@article{Hosie_2011, 
+  title={CEAMARC, the Collaborative East Antarctic Marine Census for the Census of Antarctic Marine Life (IPY # 53): An overview}, 
+  volume={5}, 
+  ISSN={1873-9652}, 
+  url={http://dx.doi.org/10.1016/j.polar.2011.04.009}, 
+  doi={10.1016/j.polar.2011.04.009}, 
+  journal={Polar Science}, 
+  publisher={Elsevier BV}, 
+  author={Hosie, Graham and Koubbi, Philippe and Riddle, Martin and Ozouf-Costaz, Catherine and Moteki, Masato and Fukuchi, Mitsuo and Ameziane, Nadia and Ishimaru, Takashi and Goffart, Anne}, 
+  year={2011}, 
+  month=aug, 
+  pages={75–87} 
+}
+
+@book{bea09,
+    url = {https://www.deepreef.org/wp-content/uploads/2009/12/CEAMARCReport_Beaman2009.pdf},
+    author = {Beaman, R. J. and O'Brien, P. E. and Philip, E. and Geoscience Australia},
+    title = {Collaborative East Antarctic Marine Census (CEAMARC): post-survey report, RSV Aurora Australis Voyage 3, December 2007-January 2008},
+    year = {2009},
+    publisher = {Geoscience Australia},
+}
+
+
+@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/Ecoregionalization_tutorial/workflows/Ecoregionalization_workflow-tests.yml

@@ -0,0 +1,73 @@
+- doc: Test outline for Ecoregionalization_Workflow
+  job:
+    ceamarc_env.tsv:
+      class: File
+      path: test-data/ceamarc_env.tsv
+      filetype: tabular
+    occurrence.txt:
+      class: File
+      path: test-data/occurrence.txt
+      filetype: tabular
+    pivot_wider_jupytool_notebook.ipynb:
+      class: File
+      path: test-data/pivot_wider_jupytool_notebook.ipynb
+      filetype: ipynb
+  outputs:
+    occ_out:
+      asserts:
+        has_size: 
+          value: 48864
+          delta: 50
+    occ_env_out:
+      asserts:
+        has_size: 
+          value: 56421
+          delta: 50
+    info_out:
+      asserts:
+        has_n_columns:
+          n: 3
+    coll_pred:
+      element_tests: 
+        1_brts_pred_ceamarc:
+          asserts:
+            has_n_columns:
+              n: 4
+    coll_val:
+      element_tests: 
+        1_brts_validation_ceamarc:
+          asserts:
+            has_n_columns:
+              n: 4
+    summary:
+      asserts:
+        has_n_columns:
+          n: 3
+    taxa:
+      asserts:
+        has_n_columns:
+          n: 1
+    taxa_clean:
+      asserts:
+        has_n_columns:
+          n: 1
+    SIH_index:
+          asserts:
+            has_text:
+              text: PNG
+    databio_table:
+      asserts:
+        has_n_columns:
+          n: 4
+    SIH_plot:
+          asserts:
+            has_text:
+              text: PNG
+    cluster_points:
+      asserts:
+        has_n_columns:
+          n: 3
+    eco_map:
+          asserts:
+            has_text:
+              text: PNG