Add drug2cell tool

[Mennayousef]

Wrapping drug2cell tool into Galaxy

[bgruening]

Thanks @Mennayousef! A few comments inside, looks very good!

[bgruening]

you can use a configfile in Galaxy to store your code and reuse this.

tools-iuc/tools/scanpy/inspect.xml

Line 55 in 5199552

<configfile name="script_file"><![CDATA[

[bgruening]

Oh it seems you have reverted the configfile change.

[Mennayousef]

yeah, it was just a test to see if without configfile will pass all checks, unfortunately it is still failing the test. with this error "Test output file (expected-output/dotplot2.png) is missing. If you are using planemo, try adding --update_test_data to generate it." I tried to manually create the expected-output folder, but no luck. Although the test passes when I run local galaxy instance.

[bgruening]

You can use here type="doi" and use a doi instead.

[Mennayousef]

@bgruening Could you please help? Why the checks are failing?

[bgruening]

remove the folder expected-output and put the dotplot1 and the umap_plot.png into the test-data folder

[bgruening]

You could add here some asserts tests and check for specific keys etc in your h5ad file:

https://docs.galaxyproject.org/en/latest/dev/schema.html#has-h5-attribute

[Mennayousef]

Hi @bgruening , I get this error when I add 'has_h5_attribute' "Invalid XML: Element 'has_h5_attribute': This element is not expected."
Maybe it is only supported for certain simpler types of HDF5 files, not this type of anndata files (h5ad)

[bernt-matthias]

Can you show us what you tried?

[Mennayousef]

Yes sure, here is the commit history. Those are the minimum two keys that should be present for drug2cell to work. Mennayousef@bbf49fa

[bernt-matthias]

This should be something like:

        <output name="d2c_output" file="d2c_output.h5ad">
         <has_contents>
          <has_h5_attribute key="obs"/>
          <has_h5_attribute key="var"/>
         </has_contents>
       </output>

has_contents was missing and evertthingt needs to be in output (before you closed it immediately).

[Mennayousef]

ERROR (XSD): Invalid XML: Element 'has_h5_attribute': This element is not expected. Expected is one of ( element, discovered_dataset, assert_contents, extra_files, metadata ).

Unfortunately this doesn't work if I added them to tests section, or outputs, or both.

Do you have a working example on h5ad file ? Otherwise I think I will leave it as it is before adding has_h5_attribute

[bernt-matthias]

See here: https://github.com/galaxyproject/galaxy/blob/223f058efae1a0eca4e4b4632da0805b8758c7c1/test/functional/tools/validation_hdf5.xml#L15

[bgruening]

assert_has_h5_attribute() missing 1 required positional argument: 'value'

You are missing the value.