Add kMetaShot and DM for kMetaShot #7421

SantaMcCloud · 2025-10-30T23:22:47Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

tools/kmetashot/kmetashot.xml

paulzierep · 2025-10-31T08:36:24Z

tools/kmetashot/kmetashot.xml

+            </options>
+            <validator type="no_options" message="No reference data for kMetaShot is installed. Please contact the Galaxy adminstrators to request one be installed."/>
+        </param>
+        <param argument="--ass2ref" type="float" min="0.0" value="0.0" max="1.0" label="Set ass2ref parameter" help="Ass2ref is a ratio between the number of MAG minimizers and the reference minimizers related to the assigned strain"/>


is is possible to get a better explanation on this ?

cfa9bf1 should be fine now?

tools/kmetashot/kmetashot.xml

paulzierep · 2025-10-31T08:41:30Z

tools/kmetashot/kmetashot.xml

+
+            **Output**
+
+            The Output is a collection with csv file(s) which contained the classification for the inputted bin(s)/MAG(s) 


It would be good if we could get our hands on one of these outputs to see the actual content, is it taxonomy per contig or per bin ?

e10b88e is this fine in this case?

paulzierep · 2025-10-31T08:43:07Z

data_managers/data_manager_kmetashot/data_manager/kmetashot_datamanager.xml

+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p '$out_file.extra_files_path' &&
+        #if $test != "true"
+            wget 'https://zenodo.org/records/17375120/files/kMetaShot_bacteria_archaea_2025-05-22.h5' &&


since there seem to be stable releases:
https://github.com/gdefazio/kMetaShot?tab=readme-ov-file#kmetashot-reference
I think it would be better if the admins could choose between those, that's better for reproducability

0acaf08 4d0b6eb i did make the DM dynamic so each new version can be added there and can be downloaded

data_managers/data_manager_kmetashot/data_manager_conf.xml

paulzierep · 2025-10-31T08:46:34Z

tools/kmetashot/kmetashot.xml

+        <![CDATA[
+
+            This tool is a taxonomic classifier which used a new algorithm which is alignment free.
+            The data from the input files will be transformed into bites and each base is represented by 2 bites.


L70 - 77 I think is not needed, we can just point to the github repo

0acaf08 you mean like this?

paulzierep · 2025-10-31T08:54:31Z

@SaimMomin12 @bgruening this tool requires a large DB (~22 GB) and also a lot of RAM, the devs confirm that it's technically not doable to shrink it: gdefazio/kMetaShot#7
Any idea how we could get it in ? Should we move it to @bgruening repo?

bgruening · 2025-10-31T09:00:44Z

Yes, please move, make sure the tests are working locally and then comment them out with a comment above the test.

SantaMcCloud · 2025-10-31T09:04:39Z

Yes, please move, make sure the tests are working locally and then comment them out with a comment above the test.

i can write test which would work but the Problem is that you need at least 16 GiB of RAM which my PC doesnt have so i dont know if i can run them locally

paulzierep · 2025-10-31T09:49:51Z

Yes, please move, make sure the tests are working locally and then comment them out with a comment above the test.

i can write test which would work but the Problem is that you need at least 16 GiB of RAM which my PC doesnt have so i dont know if i can run them locally

let me try ...

SantaMcCloud · 2025-10-31T10:14:09Z

Yes, please move, make sure the tests are working locally and then comment them out with a comment above the test.

i can write test which would work but the Problem is that you need at least 16 GiB of RAM which my PC doesnt have so i dont know if i can run them locally

let me try ...

Thank you when i did work send me the command line and the output so i can adapte thr wrapper to it. I will fix the review you made for the DM first then!

tools/kmetashot/kmetashot.xml

Co-authored-by: paulzierep <paul.zierep@googlemail.com>

…-iuc into add_kMetaShot

SantaMcCloud · 2025-11-04T18:48:30Z

@paulzierep can you check it again please if the changes i did was correct? The only thing i didnt add was the test for a possible local run

bernt-matthias · 2025-11-05T08:48:56Z

data_managers/data_manager_kmetashot/data_manager/kmetashot_datamanager.xml

+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '$__tool_directory__/kmetashot_database_installer.py'


Please do not add new data managers using the python wrapper. Just follow the scheme implemented for instance here https://github.com/galaxyproject/tools-iuc/blob/main/data_managers/data_manager_checkm2/data_manager/checkm2_datamanager.xml

Can you work with this also having multiple version of the data you download or only if you have 1 data which you download evreytime?

I will change it back of course since i had it first like this but the admin should have the option to download different Version.

Also the tool itself doesnt do the download like checkm2. We have to use wget in this case

Can you work with this also having multiple version of the data you download or only if you have 1 data which you download evreytime?

I will change it back of course since i had it first like this but the admin should have the option to download different Version.

There is no difference. The point is that you can implement the same actions that are currently implemented in the python wrapper in the command block:

call wget

create json file

Also the tool itself doesnt do the download like checkm2. We have to use wget in this case
Comment

Also wget is just a command line tool that we can call directly from the command block and there is not need for a python wrapper that just calls it.

Ah okay good to know. I didnt know this so i wasnt sure if this work in this case. Thank you for answering my question!

I think this should be good or not? c22e642

Yes this looks good.

tools/kmetashot/kmetashot.xml

…-iuc into add_kMetaShot

Add kMetaShot and DM for kMetaShot

3862f71

SantaMcCloud mentioned this pull request Oct 30, 2025

Add kMetaShot MAGs Taxonomic classification tool usegalaxy-eu/FAIRyMAGs#84

Open

fix test and remove unneeded file

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paulzierep reviewed Oct 31, 2025

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bernt-matthias reviewed Nov 1, 2025

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SantaMcCloud and others added 8 commits November 4, 2025 18:59

Update tools/kmetashot/kmetashot.xml

4ef6892

Co-authored-by: paulzierep <paul.zierep@googlemail.com>

Update tools/kmetashot/kmetashot.xml

7e91306

Co-authored-by: paulzierep <paul.zierep@googlemail.com>

Update data_managers/data_manager_kmetashot/data_manager_conf.xml

a961b6c

Co-authored-by: paulzierep <paul.zierep@googlemail.com>

make file names shell safe

2953837

Merge branch 'add_kMetaShot' of https://github.com/SantaMcCloud/tools…

5e9d599

…-iuc into add_kMetaShot

change help text for param

cfa9bf1

more information about the output

e10b88e

rewrote DM and change help section

0acaf08

SantaMcCloud added 5 commits November 4, 2025 19:50

add pyscript

4d0b6eb

fix test

6a8350d

fix linting

a56eec4

typo

0acc0e1

fix assert_content in test

be65946

bernt-matthias reviewed Nov 5, 2025

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SantaMcCloud added 4 commits November 5, 2025 16:39

change DM to a single file tool

c22e642

remove .py file§

61157d7

chage profile version

ed60219

remove output label

e3d8e77

SantaMcCloud and others added 10 commits November 5, 2025 16:42

change single quotes to double quotes

a230944

restart test

102fb8f

fix test

2ed91cf

Merge branch 'add_kMetaShot' of https://github.com/SantaMcCloud/tools…

e9bbec2

…-iuc into add_kMetaShot

maybe test fix

b1b05c1

maybe test fix

587e629

maybe test fix

4e6cfc8

fix test

d7821e7

change download link from version 1

bd8a260

Update kmetashot.xml

77d0f1b


		Output

		The Output is a collection with csv file(s) which contained the classification for the inputted bin(s)/MAG(s)

Add kMetaShot and DM for kMetaShot #7421

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Add kMetaShot and DM for kMetaShot #7421

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SantaMcCloud commented Oct 30, 2025

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paulzierep commented Oct 31, 2025

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bgruening commented Oct 31, 2025

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