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add workflow test for single-cell raceid tutorial #5639

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merged 4 commits into from
Dec 13, 2024
Merged

add workflow test for single-cell raceid tutorial #5639

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15a43b2
add workflow test for single-cell raceid tutorial
pavanvidem Dec 13, 2024
bc3ba00
revert redirect
pavanvidem Dec 13, 2024
724ea13
change history link to single-cell lab
pavanvidem Dec 13, 2024
9822520
update workflow with authors and license
pavanvidem Dec 13, 2024
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2 changes: 1 addition & 1 deletion topics/single-cell/tutorials/scrna-raceid/data-library.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ items:
- name: 'DOI: 10.5281/zenodo.1511582'
description: latest
items:
- url: https://zenodo.org/api/files/9d07494b-b15c-4a69-baf5-1e77087586b7/intestinalData.tsv
- url: https://zenodo.org/record/1511582/files/intestinalData.tsv
src: url
ext: tabular
info: https://doi.org/10.5281/zenodo.1511582
15 changes: 11 additions & 4 deletions topics/single-cell/tutorials/scrna-raceid/tutorial.md
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Expand Up @@ -6,6 +6,10 @@ priority: 2
redirect_from:
- /topics/transcriptomics/tutorials/scrna-raceid/tutorial
zenodo_link: 'https://zenodo.org/record/1511582'
answer_histories:
- label: "UseGalaxy.eu"
history: https://singlecell.usegalaxy.eu/u/videmp/h/downstream-single-cell-rna-analysis-with-raceid
date: 2024-12-13
tags:
questions:
- What is normalisation and why is it necessary?
Expand Down Expand Up @@ -41,12 +45,15 @@ key_points:
- RaceID can be used to cluster cells based on the their gene expression profiles
- StemID describes a hierarchical relationship between clusters to find multipotent progenitor stem cells to provide an understanding of cell development
- FateID predicts the potential lineages that cells within specific clusters are inclined towards
contributors:
- mtekman
- astrovsky01

gitter: Galaxy-Training-Network/galaxy-single-cell
contributions:
authorship:
- mtekman
- astrovsky01
testing:
- pavanvidem

gitter: Galaxy-Training-Network/galaxy-single-cell

---

Expand Down
19 changes: 19 additions & 0 deletions topics/single-cell/tutorials/scrna-raceid/workflows/RaceID-Workflow-tests.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
- doc: Test outline for RaceID-Workflow
job:
Tabular Matrix:
class: File
location: https://zenodo.org/record/1511582/files/intestinalData.tsv
filetype: tabular
outputs:
outdiffgenes (Step 8):
asserts:
has_n_lines:
value: 11
has_text:
text: "Chmp1a"
text: "Dgat1"
outpdf (Step 9):
asserts:
has_size:
value: 1573003
delta: 31460
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