Merge pull request galaxyproject#445 from lldelisle/brew3r

Add BREW3R

workflows/transcriptomics/brew3r/.dockstore.yml

@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /BREW3R.ga
+  testParameterFiles:
+  - /BREW3R-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960

workflows/transcriptomics/brew3r/BREW3R-tests.yml

@@ -0,0 +1,29 @@
+- doc: Test outline for BREW3R
+  job:
+    Input gtf:
+      class: File
+      path: test-data/input.gtf
+      filetype: gtf
+    BAM collection:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: GSM4196550
+        path: test-data/GSM4196550_subset.bam
+      - class: File
+        identifier: GSM4196551
+        path: test-data/GSM4196551_subset.bam
+      - class: File
+        identifier: GSM4196552
+        path: test-data/GSM4196552_subset.bam
+    strandedness: 'stranded - reverse'
+    minimum coverage: 10
+    minimum FPKM for merge: 1.0
+  outputs:
+    extended_gtf:
+      asserts:
+        has_line:
+          line: 'chr12	HAVANA	exon	11206402	11208972	.	-	.	gene_id "ENSMUSG00000047002.2"; gene_type "protein_coding"; gene_name "Msgn1"; level "2"; mgi_id "MGI:1860483"; havana_gene "OTTMUSG00000065713.1"; transcript_id "ENSMUST00000049877.2"; transcript_type "protein_coding"; transcript_name "Msgn1-201"; protein_id "ENSMUSP00000055001.1"; transcript_support_level "NA"; tag "CCDS"; ccdsid "CCDS25814.1"; havana_transcript "OTTMUST00000159929.1"; exon_number "1"; exon_id "ENSMUSE00000372682.2.ext"'
+        has_text:
+          text: "CDS"