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Integrate another bioMLmodel (biomd0000001076) #1371

Merged

bgruening merged 18 commits into bgruening:master from anuprulez:integrate_BIOMD0000001076

Jan 5, 2024

Contributor

anuprulez commented Dec 21, 2023 •

edited

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ping @bgruening thanks!

Integrates one of the models from (#1365): BIOMD0000001076

The docker container is at: docker.io/anupkumar/biomodels_biomd0000001076:1. I could not push it to quay.io/galaxy/...

The source for building docker is at: https://github.com/anuprulez/biomodelsml-docker/tree/master/prediction_bc_mlp

anuprulez added 4 commits

December 21, 2023 12:37


          Add tool BIOMD0000001076

614f988


          update tool desc

c4306b7


          update tool desc

47a8deb


          add version

345988c

Owner

bgruening commented Dec 21, 2023

Can you look at the failing test? Anup should we move the containers to usegalaxy-eu organisation.

anuprulez added 2 commits

December 21, 2023 14:30


          update

67346d8


          update test

b50b15f

Contributor Author

anuprulez commented Dec 21, 2023

Ok, tests are fixed. I have moved the containers repo to https://github.com/usegalaxy-eu/docker-biomodels-ml

bgruening reviewed

View reviewed changes

tools/biomodelsML/biomodels_BIOMD0000001076.xml Outdated

+              data_test = pd.read_csv('$input_file', sep=",")
+              #end if
+              print(data_test)

Owner

bgruening Dec 21, 2023

The print needs to be removed?

anuprulez and others added 2 commits

December 21, 2023 15:31


          remove print

4b6e947


          add creator

cabdbe7

bgruening reviewed

View reviewed changes

tools/biomodelsML/biomodels_BIOMD0000001076.xml

+                  <macros>
+                      <token name="@VERSION@">1</token>
+                  </macros>
+                  <creator>

Owner

bgruening Dec 21, 2023

Is that ok for you?

Contributor Author

anuprulez Dec 22, 2023

yes, it works. Thanks a lot :)

bgruening reviewed

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tools/biomodelsML/biomodels_BIOMD0000001076.xml Outdated

+                  </help>
+                  <citations>
+                      <citation type="bibtex">
+                          @ARTICLE{BIOMD0000001076,

Owner

bgruening Dec 21, 2023

maybe that DOI 10.1038/s41598-020-65584-y - maybe in addition?


          update tool

4c27f2d

bgruening reviewed

View reviewed changes

tools/biomodelsML/biomodels_BIOMD0000001076.xml Outdated

                           @ARTICLE{BIOMD0000001076,
                               Author = {López-Cortés A, Cabrera-Andrade A, Vázquez-Naya JM, Pazos A, Gonzáles-Díaz H, Paz-Y-Miño C, Guerrero S, Pérez-Castillo Y, Tejera E, Munteanu CR},
                               title = {{Prediction of breast cancer proteins involved in immunotherapy, metastasis, and RNA-binding using molecular descriptors and artificial neural networks. Scientific reports , 5/ 2020 , Volume 10 , Issue 1 , pages: 8515 , PubMed ID: 32444848}},
-                              url = {https://www.ebi.ac.uk/biomodels/BIOMD0000001076}
+                              url = {https://www.ebi.ac.uk/biomodels/BIOMD0000001076},

Owner

bgruening Dec 22, 2023

What I meant is type doi.


          update doi

1ed1b14

bgruening reviewed

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tools/biomodelsML/biomodels_BIOMD0000001076.xml Outdated Show resolved Hide resolved

anuprulez and others added 7 commits

January 3, 2024 09:33


          Update tools/biomodelsML/biomodels_BIOMD0000001076.xml

672437a

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>


          Merge branch 'bgruening:master' into integrate_BIOMD0000001076

ee9cc55


          remove xlsx

48bf298


          test bibtext to fix test

27adac4


          revert to type=doi

8df994c


          remove creator tag

9fa0e1c


          update profile

86695d5

Contributor Author

anuprulez commented Jan 4, 2024

I see that the CI's lxml package is now lxml-5.0.0-cp37-cp37m-manylinux_2_28_x86_64.whl.metadata updated but in the previous successful run (https://github.com/bgruening/galaxytools/actions/runs/7299086010/job/19891280680), it was lxml-4.9.4-cp37-cp37m-manylinux_2_28_x86_64.whl.metadata. Maybe that's the cause of failing tests in planemo lint step? Locally, I am using the same planemo==0.75.19 as the CI.

lxml.etree.XMLSchemaParseError: complex type 'Output': The content model is not determinist., line 5329

Owner

bgruening commented Jan 4, 2024

This is a known problem due to a new lxml version. pip install 'lxml<5' will fix that or new Galaxy packages.

Why did you remove the creator tag?

Contributor Author

anuprulez commented Jan 4, 2024

Why did you remove the creator tag?

I was testing to resolve the lining error. I made a few changes to find the cause of the lining error in the XML like removing citations as well. Locally, planemo lint worked fine. It's all there now.

This is a known problem due to a new lxml version. pip install 'lxml<5' will fix that or new Galaxy packages.

ah, good to know :)


          update embedded script name

80e6548

bgruening approved these changes

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Owner

bgruening left a comment

Ready?

Contributor Author

anuprulez commented Jan 5, 2024

yes, I think so :)

bgruening merged commit 96a70f2 into bgruening:master

11 checks passed

anuprulez deleted the integrate_BIOMD0000001076 branch

January 5, 2024 13:55

sunyi000 pushed a commit to sunyi000/galaxytools that referenced this pull request


          Integrate another bioMLmodel (biomd0000001076) (bgruening#1371)

e239dcb

* Add tool BIOMD0000001076

* update tool desc

* update tool desc

* add version

* update

* update test

* remove print

* add creator

* update tool

* update doi

* Update tools/biomodelsML/biomodels_BIOMD0000001076.xml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* remove xlsx

* test bibtext to fix test

* revert to type=doi

* remove creator tag

* update profile

* update embedded script name

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

bgruening added a commit that referenced this pull request


          tool for wound healing scratch assay image analysis (#1356)

4d4d0b1

* woundhealing tool

* added gitlab citation

* fixing typo

* remove unwanted file

* add .shed.yml

* added location tag in tests

* clean test data

* update shed.yml

* Fix two bugs with `split_file_to_collection` (#1358)

* fix two bugs

* allow chunksize to be greater than the number of records in the input file without failing
* allow an empty file to be split without an error

* bump version number

* Update Nanopolish to v0.14 (#1359)

* fix lint error + version upgrade

* Explicit untar of .tar.xz

* Adapt tests to multithreading and code refactoring

* Add RBPBench tool wrapper (#1360)

* add wrapper files

* add macros

* modify select_rbps command

* add fasta_indexes.loc

* fix data_table and genome fasta path

* new conda version with wrapper script

* new conda version with wrapper script

* remove python_template_version

---------

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

* update rbpbench tool-data conf (#1362)

* Add palette options to convert (#1364)

* tool to query ftplinks from bioimage archive (#1345)

* added tool to query ftplink from bia

* multiple values

* add help

* add .shed.yml;remove multiple from param

* remove wrong file

* updates to the tool

* Update biaftplink.xml

* Update .shed.yml

* Update biaftplink.xml

---------

Co-authored-by: Yi Sun <ysun@embl.de>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* update v08 to fix meme version check error (#1366)

* add mavedb data source tool (#1367)

* add mavedb data source tool

* Rename shed.yml to .shed.yml

* change category

* remove duplicate category

* change tool ID to mavedb_importer

* Update tools/mave_tools/mavedb/.shed.yml

* Update mavedb.xml

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Change query params according mavedb requirements (#1368)

* add mavedb data source tool

* Rename shed.yml to .shed.yml

* change category

* remove duplicate category

* change tool ID to mavedb_importer

* Update tools/mave_tools/mavedb/.shed.yml

* Update mavedb.xml

* change param names for mavedb requirements

* remove comment

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern.gruening@gmail.com>

* update to v081 (#1369)

* gm updates (#1373)

* gm updates

* fix linting

* Update compare.xml

* Integrate another bioMLmodel (biomd0000001076) (#1371)

* Add tool BIOMD0000001076

* update tool desc

* update tool desc

* add version

* update

* update test

* remove print

* add creator

* update tool

* update doi

* Update tools/biomodelsML/biomodels_BIOMD0000001076.xml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* remove xlsx

* test bibtext to fix test

* revert to type=doi

* remove creator tag

* update profile

* update embedded script name

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* fix typo in param documentation (#1374)

* bump intarna 3.4.0 (#1378)

* Updating tools/cpat from version 3.0.4 to 3.0.5 (#1379)

Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>

* Updating tools/image_processing/graphicsmagick from version 1.3.40 to 1.3.42 (#1380)

Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>

* Cool to hic (#1382)

* adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker
It actually does work. Sort of.
Hope this is useful to someone.

* fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :)

* add yara mapper ToolFactory - NOT from nf-core.
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

* small test files still work :)

* single quotes for $runme - disappeared mysteriously :(

* adding panaroo

* Finally fixed the '$runme' suggestion and got the sanitisers not to.

* fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement...

* cool_to_hic tool

* add cool_to_hic

* cleanup other branch

* fix bogus gfastats fix

* fix gfastats

* and again

* fix yaml

* fix so allows cool/mcool/scool - untested as I got no data...

* need test data.

* fixes from review

* fix bogus help transition

* Update .shed.yml

* some small cleanups

* Update .shed.yml

* lets call it juicebox_hic

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Add juicebox_hic format and citation (#1383)

* adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker
It actually does work. Sort of.
Hope this is useful to someone.

* fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :)

* add yara mapper ToolFactory - NOT from nf-core.
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

* small test files still work :)

* single quotes for $runme - disappeared mysteriously :(

* adding panaroo

* Finally fixed the '$runme' suggestion and got the sanitisers not to.

* fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement...

* add citation and link to github
add juicebox_hic as the name of the output

* fix branch again

* update CI

* Add TAPscan (#1357)

* add tapscan tool

* update shed file for this repo

* add edam topic and creator

* compress domains file

* AGAT - Add new feature (functional annotation) (#1377)

* add new feature

* small modifications

* some modification

* small changes

* small modifications

* small modification

* small modification

---------

Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>

* update CI

* update CI

* Tapscan update (#1388)

* add new updated tapscan files

* update wrapper and test data

* change fiji-mopholibj version

* small cleanups

* Update woundhealing.xml

---------

Co-authored-by: Yi Sun <ysun@embl.de>
Co-authored-by: Simon Bray <32272674+simonbray@users.noreply.github.com>
Co-authored-by: Tunc Kayikcioglu <19364610+tuncK@users.noreply.github.com>
Co-authored-by: Michael Uhl <uhl.michael@gmx.de>
Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>
Co-authored-by: Helena <hexylena@galaxians.org>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Polina Polunina <55543056+PlushZ@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern.gruening@gmail.com>
Co-authored-by: Anup Kumar <kumara@informatik.uni-freiburg.de>
Co-authored-by: Linelle <48773001+abueg@users.noreply.github.com>
Co-authored-by: Martin Raden <mmann@informatik.uni-freiburg.de>
Co-authored-by: gxydevbot <72021197+gxydevbot@users.noreply.github.com>
Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Co-authored-by: Ross Lazarus <fubar2@users.noreply.github.com>
Co-authored-by: Saskia Hiltemann <shiltemann@users.noreply.github.com>
Co-authored-by: Rlibouban <127295521+rlibouba@users.noreply.github.com>

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