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update workflows and tests
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@lldelisle
lldelisle committed Apr 28, 2023
1 parent f26c047 commit 36eb5cf
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149 changes: 123 additions & 26 deletions topics/transcriptomics/tutorials/ref-based/workflows/deg-analysis-test.yml
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Original file line number Diff line number Diff line change
@@ -1,46 +1,45 @@
---
- doc: "Test sample data for Transcriptomics:Refence-based"
- doc: "Test sample data for Transcriptomics:Refence-based - DEG"
job:
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz:
class: File
# Can be uncommented when https://github.com/galaxyproject/galaxy/pull/16014 is introduced to server
# location: https://zenodo.org/record/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz
# decompress: true
filetype: gtf
path: test-data/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf
Input Dataset Collection:
class: Collection
collection_type: list
elements:
- class: File
identifier: GSM461176_untreat_single
location: https://zenodo.org/record/1185122/files/GSM461176_untreat_single.counts
location: https://zenodo.org/record/6457007/files/GSM461176_untreat_single_featureCounts.counts
filetype: tabular
- class: File
identifier: GSM461177_untreat_paired
location: https://zenodo.org/record/1185122/files/GSM461177_untreat_paired.counts
location: https://zenodo.org/record/6457007/files/GSM461177_untreat_paired_featureCounts.counts
filetype: tabular
- class: File
identifier: GSM461178_untreat_paired
location: https://zenodo.org/record/1185122/files/GSM461178_untreat_paired.counts
location: https://zenodo.org/record/6457007/files/GSM461178_untreat_paired_featureCounts.counts
filetype: tabular
- class: File
identifier: GSM461179_treat_single
location: https://zenodo.org/record/1185122/files/GSM461179_treat_single.counts
location: https://zenodo.org/record/6457007/files/GSM461179_treat_single_featureCounts.counts
filetype: tabular
- class: File
identifier: GSM461180_treat_paired
location: https://zenodo.org/record/1185122/files/GSM461180_treat_paired.counts
location: https://zenodo.org/record/6457007/files/GSM461180_treat_paired_featureCounts.counts
filetype: tabular
- class: File
identifier: GSM461181_treat_paired
location: https://zenodo.org/record/1185122/files/GSM461181_treat_paired.counts
location: https://zenodo.org/record/6457007/files/GSM461181_treat_paired_featureCounts.counts
filetype: tabular
- class: File
identifier: GSM461182_untreat_single
location: https://zenodo.org/record/1185122/files/GSM461182_untreat_single.counts
location: https://zenodo.org/record/6457007/files/GSM461182_untreat_single_featureCounts.counts
filetype: tabular
Drosophila_melanogaster.BDGP6.87.gtf:
class: File
location: https://zenodo.org/record/1185122/files/Drosophila_melanogaster.BDGP6.87.gtf
filetype: gtf
Drosophila_melanogaster.BDGP6.87.gene_lengths:
class: File
location: https://zenodo.org/record/1185122/files/Drosophila_melanogaster.BDGP6.87.gene_lengths
filetype: tabular
header:
class: File
path: test-data/header.txt
Expand All @@ -50,19 +49,117 @@
path: test-data/KEGG_toplot.txt
filetype: tabular
outputs:
deseq_out:
DESeq2_plots:
asserts:
has_text:
text: '1086.97429520489'
z_score:
has_size:
value: 3656746
delta: 300000
DESeq2_normalized_counts:
asserts:
has_text:
text: '1.222027'
has_n_lines:
n: 23933
has_line:
line: "FBgn0250732\t1159.72839477312\t1213.33837602726\t1244.55948687904\t1247.50499330866\t874.22856885554\t1090.77053662496\t1051.75746305442"
go_terms:
asserts:
has_text:
text: 'GO:0005576'
has_n_lines:
n: 12215
has_line:
line: "GO:0005576\t1.64668479430669e-09\t1\t109\t1064\textracellular region\tCC\t2.01126080776619e-05\t1"
go_plot:
asserts:
has_size:
value: 7183
delta: 700
go_genes:
asserts:
has_n_lines:
n: 12215
has_line:
line: "GO:0005978\tFBGN0003076,FBGN0266064,FBGN0036862,FBGN0020618,FBGN0053138,FBGN0034950,FBGN0011754,FBGN0265191"
kegg_pathways:
asserts:
has_text:
text: '01100'
has_n_lines:
n: 128
has_line:
line: "00010\t2.05063769648692e-05\t0.999996086029403\t14\t47\t0.00260430987453839\t1"
kegg_genes:
asserts:
has_n_lines:
n: 128
has_line:
line: "04512\tFBGN0029167,FBGN0029896,FBGN0000299,FBGN0016075"
go_overrepresented:
asserts:
has_n_lines:
n: 60
has_line:
line: "GO:0005576\t1.64668479430669e-09\t1\t109\t1064\textracellular region\tCC\t2.01126080776619e-05\t1"
kegg_overrepresented:
asserts:
has_n_lines:
n: 2
has_line:
line: "00010\t2.05063769648692e-05\t0.999996086029403\t14\t47\t0.00260430987453839\t1"
DESeq2_annotated_results_with_header:
asserts:
has_n_lines:
n: 23933
has_line:
line: "FBgn0025111\t1508.08707143002\t2.6803835034663\t0.099224531264837\t27.013314845622\t1.0310095197245e-160\t2.22981583878416e-157\tchrX\t10778953\t10786907\t-\tprotein_coding\tAnt2"
z_score:
asserts:
has_n_lines:
n: 23933
has_line:
line: "FBgn0250732\t0.251834\t0.651925\t0.884927\t0.906910\t-1.878847\t-0.262797\t-0.553951"
go_underrepresented:
asserts:
has_n_lines:
n: 7
has_line:
line: "GO:0016071\t0.999997512116942\t7.82099466455627e-06\t12\t444\tmRNA metabolic process\tBP\t1\t0.0136465184046986"
kegg_underrepresented:
asserts:
has_n_lines:
n: 0
go_underrepresented_categories:
asserts:
- that: "has_n_lines"
n: 2
- that: "has_line"
line: "BP\t5"
- that: "has_line"
line: "CC\t2"
go_overrepresented_categories:
asserts:
- that: "has_n_lines"
n: 3
- that: "has_line"
line: "BP\t50"
- that: "has_line"
line: "CC\t5"
- that: "has_line"
line: "MF\t5"
heatmap_log:
asserts:
has_size:
value: 27113
delta: 2000
heatmap_zscore:
asserts:
has_size:
value: 27173
delta: 2000
pathview_plot:
element_tests:
dme00010:
asserts:
has_size:
value: 31803
delta: 3000
dme03040:
asserts:
has_size:
value: 61695
delta: 6000
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