Merge pull request #4072 from galaxyproject/beer-data-analysis-tutorial-update

Update beer data analysis tutorial

Author: shiltemann

topics/metagenomics/tutorials/beer-data-analysis/images/beerdecoded.gif

@@ -1,13 +1,25 @@
 
+@article{bellon2013introducing,
+  title={Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae},
+  author={Bellon, Jennifer R and Schmid, Frank and Capone, Dimitra L and Dunn, Barbara L and Chambers, Paul J},
+  journal={PLoS one},
+  volume={8},
+  number={4},
+  pages={e62053},
+  year={2013},
+  publisher={Public Library of Science San Francisco, USA},
+  doi={10.1371/journal.pone.0062053}
+}
+
 @article{Chen_2018,
-doi = {10.1101/274100},
-publisher = {Cold Spring Harbor Laboratory},
-title = {fastp: an ultra-fast all-in-one {FASTQ} preprocessor},
-url = {https://doi.org/10.1101%2F274100},
-author = {Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
-date = {2018-03},
-year = {2018},
-month = {3},
+  doi = {10.1101/274100},
+  publisher = {Cold Spring Harbor Laboratory},
+  title = {fastp: an ultra-fast all-in-one {FASTQ} preprocessor},
+  url = {https://doi.org/10.1101%2F274100},
+  author = {Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
+  date = {2018-03},
+  year = {2018},
+  month = {3},
 }
 
 @article{delahaye2021sequencing,
@@ -18,7 +30,8 @@ @article{delahaye2021sequencing
   number={10},
   pages={e0257521},
   year={2021},
-  publisher={Public Library of Science San Francisco, CA USA}
+  publisher={Public Library of Science San Francisco, CA USA},
+  doi={10.1371/journal.pone.0257521}
 }
 
 
@@ -30,22 +43,23 @@ @article{kurtzman1994molecular
   number={13},
   pages={1727--1740},
   year={1994},
-  publisher={Wiley Online Library}
+  publisher={Wiley Online Library},
+  doi={10.1002/yea.320101306}
 }
 
 
 @article{Ondov_2011,
-journal = {BMC Bioinformatics},
-doi = {10.1186/1471-2105-12-385},
-number = {1},
-publisher = {Springer Science and Business Media LLC},
-title = {Interactive metagenomic visualization in a Web browser},
-url = {https://doi.org/10.1186%2F1471-2105-12-385},
-volume = {12},
-author = {Ondov, Brian D and Bergman, Nicholas H and Phillippy, Adam M},
-date = {2011-09},
-year = {2011},
-month = {9},
+  journal = {BMC Bioinformatics},
+  doi = {10.1186/1471-2105-12-385},
+  number = {1},
+  publisher = {Springer Science and Business Media LLC},
+  title = {Interactive metagenomic visualization in a Web browser},
+  url = {https://doi.org/10.1186%2F1471-2105-12-385},
+  volume = {12},
+  author = {Ondov, Brian D and Bergman, Nicholas H and Phillippy, Adam M},
+  date = {2011-09},
+  year = {2011},
+  month = {9},
 }
 
 @article{sampaio2018microbe,
@@ -56,7 +70,19 @@ @article{sampaio2018microbe
   number={9},
   pages={1069},
   year={2018},
-  publisher={Microbiology Society}
+  publisher={Microbiology Society},
+  doi={10.1099/mic.0.000677}
+}
+
+@article{sobel2017beerdecoded,
+  title={BeerDeCoded: the open beer metagenome project},
+  author={Sobel, Jonathan and Henry, Luc and Rotman, Nicolas and Rando, Gianpaolo},
+  journal={F1000Research},
+  volume={6},
+  pages={1676},
+  year={2017},
+  publisher={F1000 Research Limited London, UK},
+  doi={10.12688/f1000research.12564.2}
 }
 
 
@@ -81,5 +107,6 @@ @article{wood2019improved
   number={1},
   pages={1--13},
   year={2019},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1186/s13059-019-1891-0}
 }

topics/metagenomics/tutorials/beer-data-analysis/images/krona.png

@@ -0,0 +1,16 @@
+---
+- doc: Test for the workflow
+  job:
+    input:
+      class: File
+      location: https://zenodo.org/record/7093173/files/ABJ044_c38189e89895cdde6770a18635db438c8a00641b.fastq
+      filetype: fastqsanger
+  outputs:
+    kraken_report:
+      asserts:
+        has_text:
+          text: 'Saccharomyces cerevisiae'
+    krakentool_report:
+      asserts:
+        has_text:
+          text: 's__Saccharomyces_cerevisiae'