Merge pull request galaxyproject#5236 from Delphine-L/decontamination

Creation of a tutorial for Asssembly decontamination

topics/assembly/tutorials/assembly-decontamination/data-library.yaml

@@ -0,0 +1,19 @@
+---
+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: Decontamination of a genome assembly
+    items:
+    - name: 'DOI: 10.5281/zenodo.13367433'
+      description: latest
+      items: 
+        - info: https://doi.org/10.5281/zenodo.13367433
+          url: https://zenodo.org/records/13367433/files/Contaminated_assembly.fasta
+          ext: fasta
+          src: url

topics/assembly/tutorials/assembly-decontamination/faqs/index.md

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

topics/assembly/tutorials/assembly-decontamination/tutorial.bib

@@ -0,0 +1,60 @@
+
+# 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}
+}
+
+@article{saini2016gene,
+  title={Gene masking-a technique to improve accuracy for cancer classification with high dimensionality in microarray data},
+  author={Saini, Harsh and Lal, Sunil Pranit and Naidu, Vimal Vikash and Pickering, Vincel Wince and Singh, Gurmeet and Tsunoda, Tatsuhiko and Sharma, Alok},
+  journal={BMC Medical Genomics},
+  volume={9},
+  pages={261--269},
+  year={2016},
+  publisher={Springer},
+  doi = {10.1186/s12920-016-0233-2}
+}
+
+@online{maskedref-website,
+  author = {Derek Caetano-Anolles},
+  title = {Masked reference genomes},
+  url = {https://gatk.broadinstitute.org/hc/en-us/articles/17295731870235-Masked-reference-genomes},
+  urldate = {2024-08-14}
+}