Merge pull request #4481 from galaxyproject/whale-acoustic

add circos microbial plot tutorial
galaxyproject · Nov 8, 2023 · e76855a · e76855a
2 parents f8b1dfc + f68a02c
commit e76855a
Show file tree

Hide file tree

Showing 9 changed files with 1,073 additions and 0 deletions.
diff --git a/bin/lint.rb b/bin/lint.rb
@@ -403,6 +403,7 @@ def self.snippets_too_close_together(contents)
     'cat1',
     'comp1',
     'gene2exon1',
+    'gff2bed1',
     'intermine',
     'join1',
     'param_value_from_file',

diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md
@@ -90,6 +90,8 @@ pathway:
     tutorials:
       - name: circos
         topic: visualisation
+      - name: circos-microbial
+        topic: visualisation
 
   - section: "Year 3: Introduction to Visualisation with R and Python"
     description: |

diff --git a/topics/visualisation/tutorials/circos-microbial/images/montage.gif b/topics/visualisation/tutorials/circos-microbial/images/montage.gif
diff --git a/topics/visualisation/tutorials/circos-microbial/images/plot.png b/topics/visualisation/tutorials/circos-microbial/images/plot.png
diff --git a/topics/visualisation/tutorials/circos-microbial/tutorial.md b/topics/visualisation/tutorials/circos-microbial/tutorial.md
diff --git a/topics/visualisation/tutorials/circos-microbial/workflows/index.md b/topics/visualisation/tutorials/circos-microbial/workflows/index.md
@@ -0,0 +1,3 @@
+---
+layout: workflow-list
+---
diff --git a/topics/visualisation/tutorials/circos-microbial/workflows/main_workflow-test.yml b/topics/visualisation/tutorials/circos-microbial/workflows/main_workflow-test.yml
@@ -0,0 +1,31 @@
+- doc: Test outline for Circos-for-E.-Coli
+  job:
+    Genome:
+      class: File
+      location: https://zenodo.org/record/3591856/files/genome.fa
+      filetype: fasta
+    Genes:
+      class: File
+      location: https://zenodo.org/record/3591856/files/genes%20(NCBI).gff3
+      filetype: gff3
+    RNA Seq Coverage (1):
+      class: File
+      location: https://zenodo.org/record/3591856/files/RNA-Seq%20coverage%201.bw
+      filetype: bigwig
+    RNA Seq Coverage (2):
+      class: File
+      location: https://zenodo.org/record/3591856/files/RNA-Seq%20coverage%202.bw
+      filetype: bigwig
+    DNA Sequencing Coverage:
+      class: File
+      location: https://zenodo.org/record/3591856/files/dna%20sequencing%20coverage.bw
+      filetype: bigwig
+    Variants:
+      class: File
+      location: https://zenodo.org/record/3591856/files/variants.vcf
+      filetype: vcf
+  outputs:
+    plot:
+      path: test-data/plot.png
+      compare: sim_size
+      delta: 300000 # This is so large because the GTN will automatically optimise the PNGs which destroy's this test.