New tool addition: Samestr2

[xens25]

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)

[xens25]

Hi @SaimMomin12 could I get an initial review of the tools? I was able to solve the failing tests in the PR. I still get a lint error that I do not get in the terminal so I'm unsure on how to fix it.

[SaimMomin12]

Hi @xens25

Following up. I’ve added a few preliminary inline comments. We’ll need to build a data manager for samestr_db, which can then be reused downstream across the other tools.

[xens25]

Hi @SaimMomin12 , I have now added the samestr_db as a data manager. Let me know in case there's further things to modify. Thanks in advanced.

[SaimMomin12]

Hi @SaimMomin12 , I have now added the samestr_db as a data manager. Let me know in case there's further things to modify. Thanks in advanced.

@xens25 Thanks, could you create a seperate PR for the DM?

[xens25]

Hi @wm75 , let me know in case more changes need to be done. Thanks in advance!

[wm75]

@xens25 I fixed up everything including another refactoring of the filter wrapper which is now back at consuming single datasets.

Remaining tasks for you would be to:

• test everything carefully by hand (with planemo serve)
• write some additional tests (like for the samples-select, marker-remove and marker-keep filter options)
• fix some more wrapper help sections and param help text (in compare, stats and summarize) to avoid command line jargon. Look at convert, extract, merge, etc. and see how I did it there.

[xens25]

Hi @wm75 , I added the samples-select, marker-remove and marker-keep tests in Samestr Filter. I wasn't exactly sure which things needed to be improved in the help sections and help tags, so I just tried to change some to use similar wording that you used in the other tools. Let me know in case some still need to be improved. As for planemo serve, in Samestr convert I get for (SameStr Convert on : per-clade SNV profiles) the following: a list with 0 datasets . I'm not sure why that is since the test is the same that passed in planemo test. I think it might be related to the fact that npz files are stored not directly in out_convert but inside a subdirectory with the name of the file, in this case out_convert/phage_padded, but I'm not sure if that's the reason. The rest of the tools worked as intended.

[wm75]

SameStr Convert on : per-clade SNV profiles) the following: a list with 0 datasets . I'm not sure why that is since the test is the same that passed in planemo test.

Are you sure you configured things exactly like in that test? In particular, have you set "min_vcov" to 1? When I tried this last it was working.

[xens25]

SameStr Convert on : per-clade SNV profiles) the following: a list with 0 datasets . I'm not sure why that is since the test is the same that passed in planemo test.

Are you sure you configured things exactly like in that test? In particular, have you set "min_vcov" to 1? When I tried this last it was working.

You are right! I completely missed that, I tested it again, Samestr Convert works fine!

[wm75]

Cool! Then I don't think I have anything more to add here.

@SaimMomin12 ready from my side!

[SaimMomin12]

Cool! Then I don't think I have anything more to add here.

@SaimMomin12 ready from my side!

Many thanks @wm75 for the thorough and detailed review 🙏

[mvdbeek]

Deployment status: failure

https://github.com/galaxyproject/tools-iuc/actions/runs/24440679374

[SaimMomin12]

Unexpected HTTP status code: 500: {"err_msg":"Metadata may have been defined for some items in revision '5e4329e09b16'. Correct the following problems if necessary and reset metadata.
samestr_compare.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
samestr_convert.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
samestr_extract.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
samestr_filter.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
samestr_merge.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
samestr_stats.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
samestr_summarize.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.
","err_code":500001}

@xens25 could you check on this and create a corresponding PR?

[wm75]

@xens25 looks like we simply forgot to put the tool_data_table_conf.xml.sample file from the data manager also into the folder of the actual tools. Just copying over the file in a separate PR should be all that's needed.