Add name2taxid function from taxonkit #6146

SantaMcCloud · 2024-07-13T03:46:37Z

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)

SantaMcCloud · 2024-07-13T03:48:10Z

The .shed.yml and macros.xml are from this PR: #6085 since it is the same package. The other PR was not merged yet. Also the two flags can not be tested because of the mock DB but both are working fine with a real DB.

@paulzierep

bgruening · 2024-07-13T18:54:37Z

tools/taxonkit/test-data/ncbi_taxonomy.loc

please name this file .test

bgruening · 2024-07-13T18:55:22Z

tools/taxonkit/taxonkit_name2taxid.xml

+            help="Input the column value in which the name are written. The first column is 1 and so on. (Default: 1)" />
+        <param argument="--sci-name" type="boolean" falsevalue="" truevalue="--sci-name" checked="false" label="Only searching scientific names"/>
+        <param argument="--show-rank" type="boolean" falsevalue="" truevalue="--show-rank" checked="false" label="Show rank" />
+		<conditional name="data">


the indentation is really off here ... can you please use the https://github.com/galaxyproject/galaxy-language-server and use the autoformat option

i think it should be fix now but im not sure but it look better now at least at this postion where you tag it

Its broken again. Please use the https://github.com/galaxyproject/galaxy-language-server plugin, this will help you a lot and also fixes all the formatting for you.

I used this add-on, but is does nothing on my side... I save the file and at this moment they should auto format it, which it didn't do. Also, it seems that the file which I uploaded always was not the file showed here with the broken format. I had the format on my side always correct, but it was shown always broken here on GitHub, which is strange. I now edited manually over GitHub in the hope that the format is now correct!

Ctrl+Shift+P and then format the document and "Galaxy tool: sort the attributes of all...".

You are using TABS and should use 4-spaces. Uploading the document does not change the content.

okay it should be done now with 5e4af94 .

Sorry for this stupid thing!

bgruening · 2024-07-13T18:56:19Z

tools/taxonkit/taxonkit_name2taxid.xml

+    <inputs>
+        <param name="input" type="data" format="tabular" label="Input file"
+            help="Input any tsv file where the NCBI names are written. You can also use a .txt but only one name per row!" />
+        <param argument="--name-field" type="integer" value="1" min="0" label="Column with the names" optional="false"


can you use the data_column here https://docs.galaxyproject.org/en/latest/dev/schema.html#data-column

paulzierep · 2024-07-22T08:21:01Z

tools/taxonkit/taxonkit_name2taxid.xml

+			</conditional>
+			<param name="sci_name" value="true"/>
+			<param name="show_rank" value="true"/>
+			<output name="output">


Can u please compare the output generated by the tool.

Done with 855fae6

paulzierep

Minor changes, then good from my side

paulzierep · 2024-07-30T10:22:33Z

tools/taxonkit/taxonkit_name2taxid.xml

+        <param argument="--name-field" type="data_column" data_ref="input" label="Select column with the names"
+            help="Select the colum where the name are written" />
+        <param argument="--sci-name" type="boolean" falsevalue="" truevalue="--sci-name" checked="false" label="Only searching scientific names"/>
+        <param argument="--show-rank" type="boolean" falsevalue="" truevalue="--show-rank" checked="false" label="Show rank" />


Can you specify what this shows ? Does it include the rank like this _g ? Maybe show a small example in the help.

tools/taxonkit/taxonkit_name2taxid.xml

paulzierep · 2024-07-30T10:28:11Z

tools/taxonkit/taxonkit_name2taxid.xml

+        <data name="output" format="tabular" label="Names2taxID" />
+    </outputs>
+    <tests>
+        <test>


can u add a test for the rank option

There is no way i can add this since i need special lines from the original database and i dont know how they work together to get the rank option. I did add an example in the help section to show how the output should look it you use a complete database

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

…into taxonkit

The format was not boken on my side so i try to fix in here in GitHub now. I hope this is better now

... maybe now the format is fixed

paulzierep

Minor text changes, looks good otherwise

tools/taxonkit/taxonkit_name2taxid.xml

paulzierep · 2024-08-14T13:43:47Z

tools/taxonkit/taxonkit_name2taxid.xml

+            ln -s '$taxdump' 'taxdump.tar.gz' &&
+            tar -xf 'taxdump.tar.gz' -C '.' &&
+        #else:
+            ln -s '$ncbi.fields.path/names.dmp' 'names.dmp' &&


do we still need delnodes.dmp and names.dmp in the test-db if we only use the test.tar.gz

No, i will remove it,

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

SantaMcCloud · 2024-08-14T13:59:39Z

@paulzierep all open reviews should be done

paulzierep · 2024-08-14T14:03:44Z

Good from my side @bgruening ?

SantaMcCloud · 2024-08-14T14:07:41Z

oh wait yes we need the .dmp file for the other wrapper

SantaMcCloud · 2024-08-14T14:12:26Z

Now we are good!

bgruening · 2024-08-14T14:17:35Z

tools/taxonkit/taxonkit_name2taxid.xml

+        <param argument="--show-rank" type="boolean" falsevalue="" truevalue="--show-rank" checked="false" label="Show rank" help="Use this option to yield the rank of the name in the output. For an example look at the help section!"/>
+        <conditional name="data">
+            <param name="is_select" type="select" label="Use either a cached NCBI database or provide a downloaded version.">
+                <option value="dm">Cached database</option>


That is really just nitpicking. But since those params are exposed to users in workflows etc ... can we rename the dm to cached.

and his to history?

bgruening

LGTM, just a very small nit

SantaMcCloud · 2024-08-14T14:20:13Z

Done @bgruening

bgruening · 2024-08-14T14:27:30Z

Something is missing, all tests are failing atm.

bgruening · 2024-08-14T15:42:03Z

Unfortunately, not :(

SantaMcCloud · 2024-08-14T15:44:17Z

Yes I don't know why I will take a look at it later now I have to change the dm from @paulzierep a little bit ^^`

SantaMcCloud · 2024-08-14T16:15:19Z

Okay i now know it fails. The other tool which is in the same directory cause the failed test. I will have a look at this till tomorrow !

SantaMcCloud · 2024-08-14T16:59:59Z

@bgruening okay now is good to merge. I don't know what the tools did that they got some error.....

bgruening · 2024-08-14T17:52:37Z

Great, thanks!

mvdbeek · 2024-08-14T18:01:34Z

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/10392516487

mvdbeek · 2024-08-14T18:12:46Z

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/10392516487

SantaMcCloud · 2024-08-14T19:44:33Z

Did I do something wrong? I can, don't know how to fix it :(

bgruening · 2024-08-14T20:06:40Z

I'm looking at it. Consider it as done.

SantaMcCloud · 2024-08-14T21:34:43Z

Okay thank you!

* Add name2taxid function from taxonkit * rename file * rename file * rename file and change a param * a little fix * change the test such that files will be compared * make the name options a bit clear * did an example for the show rank option * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * test for fix * test commit * fix test * fix test * commit to fix format problems * Update taxonkit_name2taxid.xml The format was not boken on my side so i try to fix in here in GitHub now. I hope this is better now * format fix maybe * delet file for reseting it on github * add the deleted file to see if the format is fixes now * Update taxonkit_name2taxid.xml ... maybe now the format is fixed * foramted * Update tools/taxonkit/taxonkit_name2taxid.xml * change such that the newest version will be dowanloaded and unpacked for the user * change but fomrat problem * fix file format * Apply suggestions from code review * Delete tools/taxonkit/test-data/test-db/names.dmp * Delete tools/taxonkit/test-data/test-db/delnodes.dmp * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * revert deleting * change value names * fix test * now fixed --------- Co-authored-by: paulzierep <paul.zierep@googlemail.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

Add name2taxid function from taxonkit

dda83a8

bgruening reviewed Jul 13, 2024

View reviewed changes

SantaMcCloud added 4 commits July 13, 2024 21:54

rename file

698d432

rename file

28d1db1

rename file and change a param

306860f

a little fix

d3876fb

SantaMcCloud mentioned this pull request Jul 15, 2024

Add Gtdb to taxdump #6148

Merged

4 tasks

paulzierep reviewed Jul 22, 2024

View reviewed changes

change the test such that files will be compared

855fae6

paulzierep reviewed Jul 30, 2024

View reviewed changes

SantaMcCloud and others added 19 commits August 1, 2024 00:55

make the name options a bit clear

0af783a

did an example for the show rank option

022abb6

Update tools/taxonkit/taxonkit_name2taxid.xml

45b2a87

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

Update tools/taxonkit/taxonkit_name2taxid.xml

f244cdb

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

Update tools/taxonkit/taxonkit_name2taxid.xml

7d875e8

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

Update tools/taxonkit/taxonkit_name2taxid.xml

8ae7dbc

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

test for fix

ae067f4

test commit

1be6b8f

Merge branch 'main' into taxonkit

55ef8d0

Merge branch 'taxonkit' of https://github.com/SantaMcCloud/tools-iuc …

ea0ae5e

…into taxonkit

fix test

fb592ac

fix test

6cfc298

commit to fix format problems

f50f0b3

Update taxonkit_name2taxid.xml

380719b

The format was not boken on my side so i try to fix in here in GitHub now. I hope this is better now

format fix maybe

65b1996

delet file for reseting it on github

b2f8360

add the deleted file to see if the format is fixes now

f93386a

Update taxonkit_name2taxid.xml

03dc04b

... maybe now the format is fixed

foramted

5e4af94

Apply suggestions from code review

d96c35d

paulzierep reviewed Aug 14, 2024

View reviewed changes

SantaMcCloud and others added 4 commits August 14, 2024 15:58

Delete tools/taxonkit/test-data/test-db/names.dmp

ccd125e

Delete tools/taxonkit/test-data/test-db/delnodes.dmp

d44f3dd

Update tools/taxonkit/taxonkit_name2taxid.xml

214cc69

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

Update tools/taxonkit/taxonkit_name2taxid.xml

de7b816

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

revert deleting

7a9c364

bgruening reviewed Aug 14, 2024

View reviewed changes

change value names

49663eb

fix test

3d91034

now fixed

e2f9f64

bgruening merged commit 703018a into galaxyproject:main Aug 14, 2024
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Add name2taxid function from taxonkit #6146

Add name2taxid function from taxonkit #6146

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SantaMcCloud commented Jul 13, 2024

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SantaMcCloud commented Aug 14, 2024

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SantaMcCloud commented Aug 14, 2024

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mvdbeek commented Aug 14, 2024

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SantaMcCloud commented Jul 13, 2024 •

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