Add Cleaverna tool by reyhaneh-tavakoli · Pull Request #1739 · bgruening/galaxytools

reyhaneh-tavakoli · 2025-12-26T18:40:24Z

@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?

bgruening

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

bgruening · 2025-12-26T20:57:39Z

+
+    <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>


is there any other option? Otherwise, we can skip this select box isn't it?

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.

bgruening · 2025-12-26T21:00:25Z

+                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' \


would it make sense to put all those files into one FASTA file?

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.

I think that would make it much easier for us to pass in the database(s) here. One single file

bgruening · 2025-12-26T21:01:44Z

+
+                --output_dir outputs
+        #end if
+        && ls -la outputs/


remove at the end when you are finished

bgruening · 2025-12-26T21:04:03Z

+                            </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"/>


I think you can remove the validator since you restirct the main param with min/max

bgruening · 2025-12-26T21:04:39Z

+                                    <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" 


that is strange, this is a text param but you want a file?

bgruening · 2025-12-26T21:06:34Z

+                                    </repeat>
+
+                                    <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)" 


is that value correct? its a bit strange and I don't think a user can manipulate this.

bgruening · 2025-12-26T21:07:30Z

+    </outputs>
+    <tests>
+        <!-- Updated test: Training mode with all required fields -->
+        <test expect_num_outputs="2">


we need many more tests here, for each conditional at least one ... again the galaxy-lanuage server can help here and generate tests.

bgruening · 2025-12-26T21:07:45Z

+        For detailed instructions and parameter descriptions, please refer to the tool documentation.
+    </help>
+    <citations>
+        <citation type="bibtex">


you have this in your macro

Co-authored-by: Björn Grüning <[email protected]>

bgruening · 2026-01-07T15:17:12Z

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.

reyhaneh-tavakoli · 2026-01-07T18:19:42Z

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 · 2026-01-07T18:21:03Z

please remove this file

bgruening

please take the PR out of Draft mode, if you think its ready

reyhaneh-tavakoli · 2026-01-07T18:27:51Z

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.

bgruening · 2026-01-22T19:52:49Z

@reyhaneh-tavakoli if this one is ready please take it out of the draft mode.

reyhaneh-tavakoli · 2026-02-16T09:56:12Z

@bgruening
Hi Björn, I hope you are doing well. I have updated the files, but the test still failed. I don't know what the problem is, and I also have some questions regarding the parameter definitions. Would you please help me with this?

reyhaneh-tavakoli · 2026-02-18T08:21:59Z

@bgruening

Hi Björn,
I sincerely appreciate all your support throughout the tool-wrapping process.
To run this tool, I need to configure several files (in FASTA and CSV formats) that the Galaxy server should automatically use when users select specific options. Some of these files also need to be available as downloadable templates for users.
However, some of the files are larger than 1 MB, and we are encountering errors when handling them. Could you please advise me on how best to proceed? Should I upload them using a data manager?

bgruening · 2026-02-18T08:37:22Z

+        <include path="data/BCL-3.fasta"/>
+        <include path="data/BCL-4.fasta"/>
+        <include path="data/BCL-5.fasta"/>
+        <include path="data/HPBC_generated_train_dataset.csv"/>


This is one of the large files, but where is it used?

Can you check if all files are actually used?

This is one of the large files, but where is it used?

Can you check if all files are actually used?

I have reviewed and updated them. However, we still have files exceeding 1MB that are necessary as inputs for the prediction step.

reyhaneh-tavakoli · 2026-02-18T08:40:21Z

@bgruening
I also have some questions regarding a command in the tool that requires a parameter file in CSV format (--params). This file contains multiple columns that define the DNAzyme parameters, and the column headers and rows may vary depending on the mode. It would be more professional if Galaxy could generate this CSV file based on user-defined values.
Is this possible in Galaxy? Are these parameters correctly defined in my XML file? Is there a more professional or standard way to define them in Galaxy? How should I define them in the test to ensure they work correctly?

Thank you very much for your guidance.

bgruening · 2026-02-18T08:53:12Z

Would https://docs.galaxyproject.org/en/latest/dev/schema.html#data-column help?

…aset.csv#

bgruening · 2026-02-18T10:45:53Z

Forget about the file-size we can merge it with that if you like.

But planemo test is also failing, you see the error messages here; https://github.com/bgruening/galaxytools/actions/runs/22135865788

nilchia · 2026-02-28T12:25:35Z

+                --model_name "${mode_selection.training_source.model_name}" \
+                --target_files_training '${__tool_directory__}/data/HPV.fasta' '${__tool_directory__}/data/BCL-1.fasta' '${__tool_directory__}/data/BCL-2.fasta' '${__tool_directory__}/data/BCL-3.fasta' '${__tool_directory__}/data/BCL-4.fasta' '${__tool_directory__}/data/BCL-5.fasta' \
+                --params HPBC_default_params.csv \
+                --prediction_mode default \


This should be selected from prediction_prediction_mode

nilchia · 2026-02-28T12:29:08Z

+                --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' \
+                --params SARS_default_params.csv \
+                --prediction_mode default \


This should be selected from prediction_prediction_mode

nilchia · 2026-02-28T12:33:17Z

+            #else:
+                #if $mode_selection.training_source.advanced_dnazyme_params.param_source.param_mode == "manual":
+                    echo "LA,RA,CS,Tem,CA" > temp_params.csv &&
+                    #set $cs_list = ','.join($mode_selection.training_source.advanced_dnazyme_params.param_source.CS)


Is CS defined in param_source

nilchia · 2026-02-28T12:36:24Z

Thanks @reyhaneh-tavakoli. It looks like that you have used too much nested macros and sections. Is it possible to somehow reduce that?

It makes it much easier to review and help.

cheers

Co-authored-by: Amirhossein Nilchi <[email protected]>

reyhaneh-tavakoli · 2026-04-12T06:58:55Z

Thanks @reyhaneh-tavakoli. It looks like that you have used too much nested macros and sections. Is it possible to somehow reduce that?

It makes it much easier to review and help.

cheers

Hi Amir,

Thank you for reviewing my PR and for your comments and suggestions. I’ve updated the branch based on your commits. Some parts are still pending, as I need more time to focus on them after this long gap.

I’d like to reduce nested macros and sections, but I need some help with this, as well as a stable internet connection to work on it. Unfortunately, I currently have limited internet access. I’m working on it whenever I can and would really appreciate any guidance or support.

Thanks again!

Add Cleaverna tool

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bgruening reviewed Dec 26, 2025

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Update tools/rna_tools/cleaverna/cleaverna.xml

b02a0b4

Co-authored-by: Björn Grüning <[email protected]>

reyhaneh-tavakoli added 2 commits January 7, 2026 19:13

The files were updated

0963be3

The planemo/lib was deleted

abf89b2

bgruening reviewed Jan 7, 2026

View reviewed changes

The pyvenv.cfg was removed

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bgruening reviewed Jan 7, 2026

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Merge branch 'master' into cleaverna

39bb113

reyhaneh-tavakoli and others added 3 commits February 15, 2026 11:00

The XML file was updated

21d34f8

The files were updated

7396e8c

Merge branch 'bgruening:master' into cleaverna

d4836b5

bgruening and others added 5 commits February 16, 2026 21:44

Rename shed.yml to .shed.yml

b628ab6

Delete tools/rna_tools/cleaverna/data/.Rhistory

1bb465c

Merge branch 'master' into cleaverna

aa921fb

The data folder was updated

d7e238e

Merge branch 'master' into cleaverna

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bgruening reviewed Feb 18, 2026

View reviewed changes

reyhaneh-tavakoli and others added 2 commits February 18, 2026 11:23

Updated data folder and XML file

7973afa

Delete tools/rna_tools/cleaverna/data/.~lock.SARS_generated_train_dat…

b56fbbf

…aset.csv#

nilchia self-requested a review February 18, 2026 10:47

nilchia requested changes Feb 28, 2026

View reviewed changes

reyhaneh-tavakoli and others added 8 commits April 12, 2026 08:27

Merge branch 'master' into cleaverna

94fcc04

Update tools/rna_tools/cleaverna/cleaverna.xml

1183995

Co-authored-by: Amirhossein Nilchi <[email protected]>

Update tools/rna_tools/cleaverna/cleaverna.xml

9fae071

Co-authored-by: Amirhossein Nilchi <[email protected]>

Update tools/rna_tools/cleaverna/cleaverna.xml

c492b98

Co-authored-by: Amirhossein Nilchi <[email protected]>

Update tools/rna_tools/cleaverna/cleaverna.xml

86ebb75

Co-authored-by: Amirhossein Nilchi <[email protected]>

Update tools/rna_tools/cleaverna/cleaverna.xml

8bb2b1f

Co-authored-by: Amirhossein Nilchi <[email protected]>

Update tools/rna_tools/cleaverna/cleaverna.xml

57168bc

Co-authored-by: Amirhossein Nilchi <[email protected]>

Update tools/rna_tools/cleaverna/cleaverna.xml

a3327ae

Co-authored-by: Amirhossein Nilchi <[email protected]>

Merge branch 'bgruening:master' into cleaverna

b972ecc

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