Merge pull request #4597 from ColineRoyaux/main

Adding tutorial on how to clean and manage AB1 files from Sanger sequencing

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/data-library.yaml

@@ -0,0 +1,12 @@
+---
+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: 'Clean and manage Sanger sequences from raw files to aligned consensus '
+    items: []

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/faqs/index.md

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

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.bib

@@ -0,0 +1,27 @@
+
+# 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{Garavaglia2022,
+  doi = {10.1016/j.parkreldis.2022.03.007},
+  url = {https://doi.org/10.1016/j.parkreldis.2022.03.007},
+  year = {2022},
+  volume = {97},
+  pages = {52-56},
+  author = {Garavaglia B, Vallian S, Romito LM, Straccia G, Capecci M, Invernizzi F, Andrenelli E, Kazemi A, Boesch S, Kopajtich R, Olfati N, Shariati M, Shoeibi A, Sadr-Nabavi A, Prokisch H, Winkelmann J, Zech M.},
+  title = {AOPEP variants as a novel cause of recessive dystonia: Generalized dystonia and dystonia-parkinsonism},
+  journal = {Parkinsonism and related disorders}
+}
+

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST-tests.yml

@@ -0,0 +1,41 @@
+- doc: Test outline for Sanger1-:-From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST
+  job:
+    HCOI primers:
+      class: File
+      path: test-data/HCOI primers.fasta
+      filetype: fasta
+    LCOI primers:
+      class: File
+      path: test-data/LCOI primers.fasta
+      filetype: fasta
+    H sequences (Reverse):
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: B05_CHD8-III6brother-18R
+        path: test-data/H sequences (Reverse)_B05_CHD8-III6brother-18R.ab1
+      - class: File
+        identifier: D05_CHD8-III6mother-18R
+        path: test-data/H sequences (Reverse)_D05_CHD8-III6mother-18R.ab1
+      - class: File
+        identifier: F07_CHD8-III6-18R
+        path: test-data/H sequences (Reverse)_F07_CHD8-III6-18R.ab1
+    L sequences (Forward):
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: B05_CHD8-III6brother-18F
+        path: test-data/L sequences (Forward)_B05_CHD8-III6brother-18F.ab1
+      - class: File
+        identifier: C05_CHD8-III6mother-18F
+        path: test-data/L sequences (Forward)_C05_CHD8-III6mother-18F.ab1
+      - class: File
+        identifier: E07_CHD8-III6-18F
+        path: test-data/L sequences (Forward)_E07_CHD8-III6-18F.ab1
+  outputs: 
+    w_blast_output:
+      path: test-data/aligned_seqs.fasta
+    w_consensus_aligned_sequences:
+      path: test-data/blast.tabular