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bgruening
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- can you please remove the entire planemo/lib/ folder
- please add a .shed.yml
- please add https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-required-files-include for all your data files
- please add a creator https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-creator-person
tools/rna_tools/cleaverna/macros.xml
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| <xml name="training_prediction_mode"> | ||
| <param name="prediction_mode" type="select" label="Analysis mode" hidden="true"> | ||
| <option value="default" selected="true">Default - Standard cleavage site prediction</option> |
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is there any other option? Otherwise, we can skip this select box isn't it?
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is there any other option? Otherwise, we can skip this select box isn't it?
Yes, in training mode it’s just set to “default,” and we can skip it.
| echo "16,8,\"AU,GU\",23,GGCUAGCUACAACGA" >> SARS_default_params.csv && \ | ||
| cleaverna \ | ||
| --model_name "${mode_selection.training_source.model_name}" \ | ||
| --target_files_training '${__tool_directory__}/data/1.fasta' '${__tool_directory__}/data/2.fasta' '${__tool_directory__}/data/3.fasta' '${__tool_directory__}/data/4.fasta' '${__tool_directory__}/data/5.fasta' '${__tool_directory__}/data/6.fasta' '${__tool_directory__}/data/7.fasta' '${__tool_directory__}/data/8.fasta' '${__tool_directory__}/data/9.fasta' '${__tool_directory__}/data/10.fasta' '${__tool_directory__}/data/11.fasta' '${__tool_directory__}/data/12.fasta' '${__tool_directory__}/data/13.fasta' '${__tool_directory__}/data/14.fasta' '${__tool_directory__}/data/15.fasta' '${__tool_directory__}/data/16.fasta' '${__tool_directory__}/data/17.fasta' '${__tool_directory__}/data/18.fasta' '${__tool_directory__}/data/19.fasta' '${__tool_directory__}/data/20.fasta' \ |
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would it make sense to put all those files into one FASTA file?
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would it make sense to put all those files into one FASTA file?
The tool currently accepts multiple FASTA files, but I can add this option if needed.
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I think that would make it much easier for us to pass in the database(s) here. One single file
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| --output_dir outputs | ||
| #end if | ||
| && ls -la outputs/ |
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remove at the end when you are finished
| </param> | ||
| <when value="individual"> | ||
| <param name="LA" type="integer" min="1" max="50" value="15" label="LA - Left arm length" help="The length of the left binding arm of DNAzyme (1-50 nucleotides)"> | ||
| <validator type="in_range" min="1" max="50" message="Left arm length must be between 1 and 50"/> |
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I think you can remove the validator since you restirct the main param with min/max
| <option value="false">No - Hide file details</option> | ||
| </param> | ||
| <when value="true"> | ||
| <param name="training_dataset_info" type="text" value="HPBC_user_merged_num.csv" |
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that is strange, this is a text param but you want a file?
| </repeat> | ||
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| <param name="output_info" type="text" | ||
| value="📋 Output format: LA,RA,CS,Start_End_Index,Tem,CA (Start_End_Index format: target_file.fasta:start-end)" |
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is that value correct? its a bit strange and I don't think a user can manipulate this.
| </outputs> | ||
| <tests> | ||
| <!-- Updated test: Training mode with all required fields --> | ||
| <test expect_num_outputs="2"> |
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we need many more tests here, for each conditional at least one ... again the galaxy-lanuage server can help here and generate tests.
| For detailed instructions and parameter descriptions, please refer to the tool documentation. | ||
| </help> | ||
| <citations> | ||
| <citation type="bibtex"> |
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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Something went wrong here in the branch? I think you need to rebase against the latest master-git branch. Or you create a new PR with your tool. |
I updated the branch. Is the problem fixed now, or should I create a new branch? |
bgruening
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please take the PR out of Draft mode, if you think its ready
I want to add more tests and change some header words to be more user-friendly. I will take it out of draft as soon as I am done with these changes. |
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@reyhaneh-tavakoli if this one is ready please take it out of the draft mode. |
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@bgruening
Hi Bjorn, Merry Christmas!
This pull request adds the Cleaverna tool to the Galaxy platform. The tool supports two execution modes: Training and Prediction. In both modes, it requires a parameter CSV file as input. To facilitate proper usage within Galaxy, this XML file is written so that it can generate the required CSV file directly using Galaxy tools, allowing it to be passed seamlessly as input to Cleaverna.
Could you please review my PR and check whether the CSV file generation part is defined correctly?