Add ToolDistillator #5967
Add ToolDistillator #5967
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Thanks a lot @clsiguret
I added some suggestions (mostly cosmetic ones)
Co-authored-by: Bérénice Batut <[email protected]>
Co-authored-by: Bérénice Batut <[email protected]>
Co-authored-by: Bérénice Batut <[email protected]>
Co-authored-by: Bérénice Batut <[email protected]>
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Waiting for new Bioconda package : bioconda/bioconda-recipes#47472 |
…th "" around input_files/
…d not used by test
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Very good @clsiguret! I added a few nitpicking stuff inline.
I'm a bit worried about the HID usage ... maybe you can explain in some comment why you need to use the HID somewhere.
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this is empty, is it needed or should it be removed?
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this can be removed I guess?
Can you please check if all files are really needed that are included in this PR?
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Thanks. I deleted empty and/or unused files. it should be good now
| <tests> | ||
| <test expect_num_outputs="1"> <!-- TEST_1 sumarize json results --> | ||
| <param name="summarize_data" ftype="json" value="summarize/abricate_output.json,summarize/bracken_full_output.json,summarize/plasmidfinder_output.json"/> | ||
| <output name="summary_json" ftype="json" value="summarize/summarize.json" compare="sim_size"/> |
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instead of using sim_size, which is the less-stringent test that we have, its better to use asserts (in addition) https://docs.galaxyproject.org/en/latest/dev/schema.html#id146
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yes, I understand why. It's good now, I added asserts as suggested :-) thanks
| #for $i, $tool in enumerate( $tool_section.tools ) | ||
| tooldistillator | ||
| $tool.select_tool.tool_list | ||
| --hid "$tool.select_tool.input.hid" |
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please use single-quotes its safer than double-quotes
| #elif $tool.select_tool.tool_list == "tabular_file" | ||
| --analysis_software_name "$tool.select_tool.analysis_software_name" | ||
| #end if | ||
| -o "tooldistillator_folder/$($tool.select_tool.tool_list)_$(i)_output.json" |
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Thanks a lot @clsiguret |
FOR CONTRIBUTOR: