Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

pvanheus · 2025-02-22T06:47:21Z

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)

Co-authored-by: Saim Momin <[email protected]>

Mmuphin wrapper

fixed tests

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

Co-authored-by: paulzierep <[email protected]>

mak covariates optional with python

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

tools/clair3/tool_data_table_conf.xml.sample

…alaxyproject#6796) * Add support for downloading schemes, fix some data table problems, change defaults to minion defaults * Remove unneeded quotes and add more info on defaults * Remove quotes around integer parameter

* Updating tools/ncbi_datasets from version 16.41.0 to 16.42.0 * Remove trailing hyphen in macros --------- Co-authored-by: planemo-autoupdate <[email protected]>

* Add ASMplot * Add associated test-data * Minor changes to description and added single quotes to parameters

Mmuphin wrapper

tools/clair3/tool_data_table_conf.xml.sample

wm75 · 2025-02-26T11:15:25Z

@pvanheus another question while we're at it: have the model files ever changed their format?
Newly installed clair3_models are now also user-selectable for old versions of clair3 (like 0.1.11+galaxy0 installed on EU). Would they be compatible?

pvanheus · 2025-02-26T15:40:24Z

@pvanheus another question while we're at it: have the model files ever changed their format? Newly installed clair3_models are now also user-selectable for old versions of clair3 (like 0.1.11+galaxy0 installed on EU). Would they be compatible?

The model files that are built by the clair3 group (available here) have not changed since October 2021, which is before the release date of any of the versions of clair3 used in Galaxy, so it seems that the model format is very stable and definitely stable across all Galaxy tool releases.

…date_clair3

wm75 · 2025-02-27T13:10:29Z

Hmm, that was a semi-successful integration. I think things are actually correct now, just a lot of annoying in-between commits from main.

wm75 · 2025-02-27T13:15:55Z

tools/artic/tool-data/models.loc.sample

-#
-#So, all_model.loc could look something like this:
-test_model	"the_model_name"	r941_prom_hac_g360+g422	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422#This file lists the names and locations of all the clair3 model files
+#This file lists the names and locations of all the clair3 model files


this entire file still needs to be renamed to clair3_models.loc.sample I guess.
Then the tool_data_table.conf needs to be adjusted too.

wm75 · 2025-02-27T13:16:34Z

tools/clair3/clair3.xml

@@ -2,7 +2,7 @@
    <description>germline small variant caller for long-reads</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.10</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>


don't bump this version so that we can overwrite the faulty previous attempt

renu-pal and others added 30 commits November 22, 2024 22:13

mmuphin wrapper draft with errors

298cadd

Update .shed.yml

ef26199

removing long description from .shed.yml

801cc88

Update tools/mmuphin/macros.xml

f0ca96f

Co-authored-by: Saim Momin <[email protected]>

Update tools/mmuphin/macros.xml

c19da4d

Co-authored-by: Saim Momin <[email protected]>

Update tools/mmuphin/macros.xml

52076ec

Co-authored-by: Saim Momin <[email protected]>

Update tools/mmuphin/macros.xml

bab0879

Co-authored-by: Saim Momin <[email protected]>

Update tools/mmuphin/macros.xml

7c09803

Co-authored-by: Saim Momin <[email protected]>

Update tools/mmuphin/mmuphin.xml

f340c26

Co-authored-by: Saim Momin <[email protected]>

reducing CRC_abd file size and adding adjust_batch.R file

4ee8d65

adding long description into .shed.yml due to linting issue

e861c0f

Update .shed.yml

f65885e

Update .shed.yml

7fafc59

update

f79c79f

update

1b335f1

rm unneeded requs

d86e487

Merge pull request galaxyproject#4 from paulzierep/mmuphin_wrapper

47d426d

Mmuphin wrapper

changing batch value in test, as first column header is null

f815e86

removing control_output from test

f36aa66

reducing file size

090b476

Update mmuphin.xml

c5af559

fixed tests

e60c159

Merge pull request galaxyproject#5 from paulzierep/mmuphin_wrapper

9c404da

fixed tests

Update tools/mmuphin/mmuphin.xml

7c2d2d7

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

getting column names in R directly

c1b167c

Apply suggestions from code review

550cd60

removed unnecessary commented code

8d38c99

Update tools/mmuphin/mmuphin.xml

b6e9c39

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

improving help section

5109992

Update tools/mmuphin/mmuphin.xml

0c902c3

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

renu-pal and others added 12 commits January 16, 2025 14:21

Update tools/mmuphin/mmuphin.xml

663287a

Co-authored-by: paulzierep <[email protected]>

adding test with covariate=null and few other updates

a139a38

mak covariates optional with python

ed1d307

Merge pull request galaxyproject#6 from paulzierep/mmuphin_wrapper

9195bf8

mak covariates optional with python

adding test case with multiple covariates

591e5b3

Update tools/mmuphin/mmuphin.xml

fa3e8a5

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

Update tools/mmuphin/mmuphin.xml

a968744

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

suggested min max convergence value

e74fa15

adding filter in O/P and min max in conv

243f1fc

Fix up tool_data_table_conf files

d5b2dcd

Remember to save this time

a26b512

Fix columns in test-data

ef8d97b

wm75 reviewed Feb 22, 2025

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pvanheus and others added 4 commits February 24, 2025 15:04

Minor update to tools/ncbi datasets (galaxyproject#6797)

836f979

* Updating tools/ncbi_datasets from version 16.41.0 to 16.42.0 * Remove trailing hyphen in macros --------- Co-authored-by: planemo-autoupdate <[email protected]>

New tool addition: MerquryFK ASMPlot (galaxyproject#6786)

a3bca79

* Add ASMplot * Add associated test-data * Minor changes to description and added single quotes to parameters

Merge pull request galaxyproject#6584 from renu-pal/mmuphin_wrapper

9d6123a

Mmuphin wrapper

wm75 reviewed Feb 26, 2025

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tools/clair3/tool_data_table_conf.xml.sample Outdated Show resolved Hide resolved

Correct tool data table name

e44d3cd

bernt-matthias mentioned this pull request Feb 26, 2025

Fixes tests from tools/artic #6800

Open

5 tasks

hugolefeuvre and others added 6 commits February 27, 2025 12:37

Update starAMR DM version (galaxyproject#6802)

c6d65d9

Fix up tool_data_table_conf files

d5a83e7

Remember to save this time

3b548fd

Fix columns in test-data

dbdf06c

Correct tool data table name

4d11cd2

Merge branch 'update_clair3' of github.com:pvanheus/tools-iuc into up…

a3740ec

…date_clair3

wm75 reviewed Feb 27, 2025

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Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

pvanheus commented Feb 22, 2025 •

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wm75 commented Feb 26, 2025

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wm75 commented Feb 27, 2025

wm75 Feb 27, 2025

wm75 Feb 27, 2025

Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

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Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790

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