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

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

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+---
+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

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+---
+layout: faq-page
+---

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

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+
+# 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/Training-Sanger-sequences-CHD8-tests.yml

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+- doc: Test outline for Training-Sanger-sequences-CHD8
+  job:
+    Prim:
+      class: File
+      path: test-data/Prim.fasta
+      filetype: fasta
+    AOPEP_and_CHD8_sequences_20220907.zip?download=1:
+      class: File
+      path: test-data/AOPEP_and_CHD8_sequences_20220907.zip?download=1.zip
+      filetype: zip
+  outputs: 
+    w_blast_output:
+      path: test-data/aligned_seqs.fasta
+    w_consensus_aligned_sequences:
+      path: test-data/blast.tabular
+

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

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+---
+layout: workflow-list
+---

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/test-data/Prim.fasta

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+>Forward_CHD8
+GAGGTGAAAGAATCATAAATTGG
+>Reverse_CHD8
+CCCTGTGTACAAATAGCTTTTGT
+>Forward_AOPEP
+TCATGGTTCCAGGCAGAGTTATT
+>Reverse_AOPEP
+TGCTGTGACAAGCCAACCAATGG

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/test-data/aligned_seqs.fasta

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+>Reverse_CHD8
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAAAAGCTATTTGTACACAGGG-----------------
+>consensus_05_CHD8-III6mother-18
+---------GAGGTGAAAGAATCATAAATTGGTATTTTGTATCCTTTCCCTTGCTAATTTTATGATATCTTTCTCCTTTCCTTTCGTTTTTATTTTAAACCAGGCCCAGGCACGATGTCATCGAATTGGGCAGAGCAAAGCTGTGAAGGTGTACCGCCTCATCACTCGTAATTCCTACGAGAGAGAGATGTTTGATAAGGCCAGCCTCAAGTTGGGGTTGGATAAGGCTGTGCTTCAATCCATGAGTGGTCGGGATGGCAACATTACTGGAGTGAGTCCTCTTAGTTTATAGATWAGTTTGTAGTAGATCATTGTGATAGAGGGAAACAAAAGCTATTTGTACACAGGGAT---------------
+>consensus_07_CHD8-III6-18
+TGCTCTATAGAGGTGAAAGAATCATAAATTGGTATTTTGTATCCTTTCCCTTGCTAATTTTATGATATCTTTCTCCTTTCCTTTCGTTTTTATTTTAAACCAGGCCCAGGCACGATGTCATCGAATTGGGCAGAGCAAAGCTGTGAAGGTGTACCGCCTCATCACTCGTAATTCCTACGAGAGAGAGATGTTTGATAAGGCCAGCCTCAAGTTGGGGTTGGATAAGGCTGTGCTTCAATCCATGAGTGGTCGGGATGGCAACATTACTGGAGTGAGTCCTCTTAGTTTATAGATAAGTTTGTAGTAGATCATTGTGATAGAGGGAAACAAAAGCTATTTGTACACAGGGATTTGACTACCTTATTA
+>consensus_B05_CHD8-III6brother-18
+------ATAGAGGTGAAAGAATCATAAATTGGTATTTTGTATCCTTTCCCTTGCTAATTTTATGATATCTTTCTCCTTTCCTTTCGTTTTTATTTTAAACCAGGCCCAGGCACGATGTCATCGAATYGGGCAGAGCAAAGCTGTGAAGGTGTACCGCCTCATCACTCGTAATTCCTACGAGAGAGAGATGTTTGATAAGGCCAGCCTCAAGTTGGGGTTGGATAAGGCTGTGCTTCAATCCATGAGTGGTCGGGATGGCAACATTACTGGAGTGAGTCCTCTTAGTTTATAGATAAGTTTGTAGTAGATCATTGTGATAGAGGGAAACAAAAGCTATTTGTACACAGGGAT---------------
+>Forward_CHD8
+---------GAGGTGAAAGAATCATAAATTGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/test-data/blast.tabular

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+consensus_B05_CHD8-III6brother-18	99.710	1	0	0	Eukaryotic synthetic construct chromosome 14<>Eukaryotic synthetic construct chromosome 14	CP034492.1
+consensus_B05_CHD8-III6brother-18	99.710	1	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), RefSeqGene on chromosome 14	NG_021249.1
+consensus_B05_CHD8-III6brother-18	99.710	1	0	0	Human chromosome 14 DNA sequence BAC R-689J19 of library RPCI-11 from chromosome 14 of Homo sapiens (Human), complete sequence	AL161747.5
+consensus_B05_CHD8-III6brother-18	85.804	36	8	9	Canis lupus familiaris breed Labrador retriever chromosome 15a	CP050569.1
+consensus_B05_CHD8-III6brother-18	85.804	36	8	9	Canis lupus familiaris breed Labrador retriever chromosome 15b	CP050620.1
+consensus_B05_CHD8-III6brother-18	85.804	36	8	9	Canis lupus genome assembly, chromosome: 15	HG994395.1
+consensus_B05_CHD8-III6brother-18	99.415	1	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 1, mRNA	NM_001170629.2
+consensus_B05_CHD8-III6brother-18	99.415	1	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 2, mRNA	NM_020920.4
+consensus_B05_CHD8-III6brother-18	99.415	1	0	0	Synthetic construct Homo sapiens clone IMAGE:100063036, MGC:190670 chromodomain helicase DNA binding protein 8 (CHD8) mRNA, encodes complete protein	BC156439.1
+consensus_B05_CHD8-III6brother-18	99.415	1	0	0	Homo sapiens cDNA FLJ16585 fis, clone TESTI4000134, weakly  similar to Chromodomain helicase-DNA-binding protein Mi-2	AK122910.1
+consensus_05_CHD8-III6mother-18	99.708	1	0	0	Eukaryotic synthetic construct chromosome 14<>Eukaryotic synthetic construct chromosome 14	CP034492.1
+consensus_05_CHD8-III6mother-18	99.708	1	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), RefSeqGene on chromosome 14	NG_021249.1
+consensus_05_CHD8-III6mother-18	99.708	1	0	0	Human chromosome 14 DNA sequence BAC R-689J19 of library RPCI-11 from chromosome 14 of Homo sapiens (Human), complete sequence	AL161747.5
+consensus_05_CHD8-III6mother-18	85.849	34	10	11	Canis lupus familiaris breed Labrador retriever chromosome 15a	CP050569.1
+consensus_05_CHD8-III6mother-18	85.849	34	10	11	Canis lupus familiaris breed Labrador retriever chromosome 15b	CP050620.1
+consensus_05_CHD8-III6mother-18	85.849	34	10	11	Canis lupus genome assembly, chromosome: 15	HG994395.1
+consensus_05_CHD8-III6mother-18	100.000	0	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 1, mRNA	NM_001170629.2
+consensus_05_CHD8-III6mother-18	100.000	0	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 2, mRNA	NM_020920.4
+consensus_05_CHD8-III6mother-18	100.000	0	0	0	Synthetic construct Homo sapiens clone IMAGE:100063036, MGC:190670 chromodomain helicase DNA binding protein 8 (CHD8) mRNA, encodes complete protein	BC156439.1
+consensus_05_CHD8-III6mother-18	100.000	0	0	0	Homo sapiens cDNA FLJ16585 fis, clone TESTI4000134, weakly  similar to Chromodomain helicase-DNA-binding protein Mi-2	AK122910.1
+consensus_07_CHD8-III6-18	99.726	1	0	0	Eukaryotic synthetic construct chromosome 14<>Eukaryotic synthetic construct chromosome 14	CP034492.1
+consensus_07_CHD8-III6-18	100.000	0	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), RefSeqGene on chromosome 14	NG_021249.1
+consensus_07_CHD8-III6-18	99.726	1	0	0	Human chromosome 14 DNA sequence BAC R-689J19 of library RPCI-11 from chromosome 14 of Homo sapiens (Human), complete sequence	AL161747.5
+consensus_07_CHD8-III6-18	84.928	41	9	11	Canis lupus familiaris breed Labrador retriever chromosome 15a	CP050569.1
+consensus_07_CHD8-III6-18	84.928	41	9	11	Canis lupus familiaris breed Labrador retriever chromosome 15b	CP050620.1
+consensus_07_CHD8-III6-18	84.928	41	9	11	Canis lupus genome assembly, chromosome: 15	HG994395.1
+consensus_07_CHD8-III6-18	100.000	0	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 1, mRNA	NM_001170629.2
+consensus_07_CHD8-III6-18	100.000	0	0	0	Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 2, mRNA	NM_020920.4
+consensus_07_CHD8-III6-18	100.000	0	0	0	Synthetic construct Homo sapiens clone IMAGE:100063036, MGC:190670 chromodomain helicase DNA binding protein 8 (CHD8) mRNA, encodes complete protein	BC156439.1
+consensus_07_CHD8-III6-18	100.000	0	0	0	Homo sapiens cDNA FLJ16585 fis, clone TESTI4000134, weakly  similar to Chromodomain helicase-DNA-binding protein Mi-2	AK122910.1

topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/tools.yml

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+install_tool_dependencies: True
+install_repository_dependencies: True
+install_resolver_dependencies: True
+
+tools:
+- name: unzip
+  owner: imgteam
+  revisions:
+  - 57f0914ddb7b
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: filter_by_fasta_ids
+  owner: galaxyp
+  revisions:
+  - dff7df6fcab5
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: collection_element_identifiers
+  owner: iuc
+  revisions:
+  - d3c07d270a50
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: mothur_degap_seqs
+  owner: iuc
+  revisions:
+  - 6f08af23888a
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: regex_find_replace
+  owner: galaxyp
+  revisions:
+  - 503bcd6ebe4b
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: fastx_reverse_complement
+  owner: devteam
+  revisions:
+  - 6027ef51ef91
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: ab1_fastq_converter
+  owner: ecology
+  revisions:
+  - 307518fb51af
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: seqtk
+  owner: iuc
+  revisions:
+  - 3da72230c066
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: fastq_groomer
+  owner: devteam
+  revisions:
+  - 47e5dbc3e790
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: fastq_to_tabular
+  owner: devteam
+  revisions:
+  - 4b347702c4aa
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: tabular_to_fasta
+  owner: devteam
+  revisions:
+  - 0a7799698fe5
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: qiime_align_seqs
+  owner: iuc
+  revisions:
+  - e8bb88f051ec
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: aligned_to_consensus
+  owner: ecology
+  revisions:
+  - 0ccbe1c20fc3
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: mothur_merge_files
+  owner: iuc
+  revisions:
+  - 7bd37d6decd9
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/
+- name: ncbi_blast_plus
+  owner: devteam
+  revisions:
+  - 0e3cf9594bb7
+  tool_panel_section_label: Tools from workflows
+  tool_shed_url: https://toolshed.g2.bx.psu.edu/