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Music update workflows/tools #5637

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Feb 10, 2025
Merged

Music update workflows/tools #5637

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34c6467
add new workflows
hexhowells Dec 12, 2024
56fb724
Merge branch 'main' of https://github.com/hexhowells/training-materia…
hexhowells Dec 12, 2024
d0cd04b
Merge branch 'main' into music-update-tools
hexhowells Jan 20, 2025
951b000
add workflow testing
hexhowells Jan 20, 2025
dcc6185
Merge branch 'main' into music-update-tools
hexhowells Jan 22, 2025
a3d204d
update workflow tests
hexhowells Jan 23, 2025
eb3627d
add licence to workflow
hexhowells Jan 23, 2025
6efa6fb
update tool versions in tutorial
hexhowells Jan 23, 2025
06e7988
Merge branch 'main' into music-update-tools
hexhowells Jan 23, 2025
41b51b9
rename main workflow
hexhowells Feb 10, 2025
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18 changes: 9 additions & 9 deletions topics/single-cell/tutorials/bulk-music/tutorial.md
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Expand Up @@ -294,7 +294,7 @@ Here we shall build two ExpressionSet objects corresponding to the bulk and sing

> <hands-on-title>Build the Expression Set inputs</hands-on-title>
>
> 1. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3) %} with the following parameters:
> 1. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4) %} with the following parameters:
> - {% icon param-file %} *"Assay Data"*: `GSE50244bulkeset.expression.tabular` (Input dataset)
> - {% icon param-file %} *"Phenotype Data"*: `GSE50244bulkeset.phenotype.tabular` (Input dataset)
>
Expand All @@ -303,7 +303,7 @@ Here we shall build two ExpressionSet objects corresponding to the bulk and sing
> > An ExpressionSet object has many data slots, the principle of which are the experiment data (*exprs*), the phenotype data (*pData*), as well metadata pertaining to experiment information and additional annotations (*fData*).
> {: .comment}
>
> 2. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3) %} with the following parameters:
> 2. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4) %} with the following parameters:
> - {% icon param-file %} *"Assay Data"*: `EMTABesethealthy.expression.tabular` (Input dataset)
> - {% icon param-file %} *"Phenotype Data"*: `EMTABesethealthy.phenotype.tabular` (Input dataset)
>
Expand All @@ -318,7 +318,7 @@ We will now inspect these objects we just created to see what information we can
> 1. Obtain General Info about the data set
> - {% icon galaxy-eye %} Click on the `#scrna` *General Info* dataset in the history view (output of **Construct Expression Set Object** {% icon tool %})
> 1. Obtain Feature Information about the data set
> - {% tool [Inspect Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3) %} with the following parameters:
> - {% tool [Inspect Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy4) %} with the following parameters:
> > <warning-title>Danger: This tool has needs!</warning-title>
> > You may need to click the dataset from your history and drag it into the input of this tool. Some browsers don't allow this.
> {: .warning}
Expand All @@ -332,7 +332,7 @@ We will now inspect these objects we just created to see what information we can
> By inspecting the `Feature Data Table`, you should see a list of gene names.
>
> 1. Obtain the dimensions of the data set
> - {% tool [Inspect Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3) %} with the following parameters:
> - {% tool [Inspect Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy4) %} with the following parameters:
> - {% icon param-file %} *"ESet Dataset"*: `#scrna` (output of **Construct Expression Set Object** {% icon tool %})
> - *"Inspect"*: `Dimension`
>
Expand Down Expand Up @@ -383,7 +383,7 @@ It's also important that input scRNA-seq datasets (ideally) have some representa

> <hands-on-title>Task description</hands-on-title>
>
> 1. {% tool [MuSiC](toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3) %} with the following parameters:
> 1. {% tool [MuSiC](toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4) %} with the following parameters:
> - *MuSiC sometimes does not show up from the tool search box. You may need to look for it under the **Single Cell** heading
> - {% icon param-file %} *"scRNA Dataset"*: `#scrna` (output of **Construct Expression Set Object** {% icon tool %})
> - {% icon param-file %} *"Bulk RNA Dataset"*: `#bulk` (output of **Construct Expression Set Object** {% icon tool %})
Expand Down Expand Up @@ -520,7 +520,7 @@ You will need to again create ExpressionSet objects, as before.

> <hands-on-title>Build the Expression Set inputs</hands-on-title>
>
> 1. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3) %} with the following parameters:
> 1. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4) %} with the following parameters:
> - {% icon param-file %} *"Assay Data"*: `Mousebulkeset.expression.tabular` (Input dataset)
> - {% icon param-file %} *"Phenotype Data"*: `Mousebulkeset.phenotype.tabular` (Input dataset)
>
Expand All @@ -529,7 +529,7 @@ You will need to again create ExpressionSet objects, as before.
> > An ExpressionSet object has many data slots, the principle of which are the experiment data (*exprs*), the phenotype data (*pData*), as well metadata pertaining to experiment information and additional annotations (*fData*).
> {: .comment}
>
> 2. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3) %} with the following parameters:
> 2. {% tool [Construct Expression Set Object](toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4) %} with the following parameters:
> - {% icon param-file %} *"Assay Data"*: `Mousesubeset.expression.tabular` (Input dataset)
> - {% icon param-file %} *"Phenotype Data"*: `Mousesubeset.phenotype.tabular` (Input dataset)
>
Expand All @@ -541,7 +541,7 @@ You will need to again create ExpressionSet objects, as before.

> <hands-on-title>Task description</hands-on-title>
>
> 1. {% tool [MuSiC](toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3) %} with the following parameters:
> 1. {% tool [MuSiC](toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4) %} with the following parameters:
> - {% icon param-file %} *"scRNA Dataset"*: `#scrna` (output of **Construct Expression Set Object** {% icon tool %})
> - {% icon param-file %} *"Bulk RNA Dataset"*: `#bulk` (output of **Construct Expression Set Object** {% icon tool %})
> - *"Purpose"*: `Compute Dendrogram`
Expand Down Expand Up @@ -594,7 +594,7 @@ We shall use the 4 cell type groups determined by the cut off threshold in the a
>
> {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
>
> 2. {% tool [MuSiC](toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3) %} with the following parameters:
> 2. {% tool [MuSiC](toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4) %} with the following parameters:
> - **Note**
> > <warning-title>Shortcut!</warning-title>
> >
Expand Down
26 changes: 26 additions & 0 deletions topics/single-cell/tutorials/bulk-music/workflows/main_workflow-tests.yml
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@@ -0,0 +1,26 @@
- doc: Test outline for main_workflow
job:
scRNA Assay Tabular:
class: File
path: https://zenodo.org/records/5719228/files/EMTABesethealthy.expression.tabular
filetype: tabular
scRNA Phenotype Tabular:
class: File
path: https://zenodo.org/records/5719228/files/EMTABesethealthy.phenotype.tabular
filetype: tabular
Bulk RNA Assay Tabular:
class: File
path: https://zenodo.org/records/5719228/files/GSE50244bulkeset.expression.tabular
filetype: tabular
Bulk RNA Phenotype Tabular:
class: File
path: https://zenodo.org/records/5719228/files/GSE50244bulkeset.phenotype.tabular
filetype: tabular
Cell Types List: alpha,beta,delta,gamma,acinar,ductal
outputs:
out_tab (Step 8):
path: test-data/music-out_tab-step_8.tabular
out_tab (Step 10):
path: test-data/music-out_tab-step_10.tabular
out_pdf (Step 11):
path: test-data/music-out_pdf-step_11.pdf
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