Added AEGeAn toolkit #3397

gallardoalba · 2020-12-23T21:52:56Z

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)

Four tools belonging to the AEGEaN toolkit have been added:

ParsEval is a program for comparing distinct sets of gene structure annotations for the same sequence(s).
CanonGFF3 is a tool for preprocessing GFF3 data.
LocusPocus is a program for computing gene loci from one or more gene prediction sets.
GAEVAL is a program for computing coverage and integrity scores for gene models using transcript alignments.

bgruening

Is this the tool? https://bio.tools/gaeval If so can you add a bio.tools ID and edam ontologies to this tool here (probably as macros)

Please use 4 spaces indentation

tools/aegean/canongff3.xml

tools/aegean/gaeval.xml

tools/aegean/locuspocus.xml

tools/aegean/canongff3.xml

bgruening

Thanks @gallardoalba

bgruening · 2020-12-26T13:09:46Z

tools/aegean/.shed.yml

@@ -0,0 +1,14 @@
+name: suite_aegean


@gallardoalba if you have multiple tools in such a suite, please use a suite-shed.yml file ... example here: https://github.com/galaxyproject/tools-iuc/blob/master/tools/hyphy/.shed.yml

Could you give me more details about which part should I modify? Should I just need to add it?
auto_tool_repositories: name_template: "{{ tool_id }}" description_template: "Wrapper for the HyPhy batch operation: {{ tool_name }}"

Please see here: https://planemo.readthedocs.io/en/latest/standards/docs/best_practices/shed_yml.html#advanced-parameters

Also there are a lot of examples in this repo.

I modified it; I guess that now is correct.

Please see here: https://github.com/galaxyproject/tools-iuc/blob/master/tools/dada2/.shed.yml (note that the duplicate category entry is not necessary).

Thanks @bernt-matthias, when should I use auto_tool_repositories in the .shed.yml file? I read about it but I'm confused because it does not appear in many cases.

I think it's the way to go if you want to add a set of tools in a single directory.

I think that now it fits with that structure.

tools/aegean/canongff3.xml

tools/aegean/gaeval.xml

tools/aegean/locuspocus.xml

tools/aegean/parseval.xml

tools/aegean/canongff3.xml

tools/aegean/gaeval.xml

tools/aegean/locuspocus.xml

bgruening · 2020-12-28T16:47:19Z

Test file canon-output_test3.gff3 is missing and one other test is failing with Please only use letters, numbers or underscores in sample label

tools/aegean/locuspocus.xml

tools/aegean/gaeval.xml

Test variable format. Co-authored-by: M Bernt <[email protected]>

gallardoalba · 2020-12-30T11:47:25Z

Great work @gallardoalba

A few more comments from my side .. I consider all of them as optional. The tools are already good to go.

Just let us know if you want to implement any of them or not.

Sure, I'll include it.

bernt-matthias · 2021-01-01T20:15:06Z

Hi @gallardoalba I fixed the outputtype problem here: 3859099

Could you also use argument instead of name as in 37fed22 (and edba35e) in the other tools. The name is generated automatically and the advantage is that the user will see the argument in the parameter help.

bernt-matthias · 2021-01-01T22:27:29Z

Btw. is it intended that sections are not expanded?

gallardoalba · 2021-01-02T16:28:05Z

Btw. is it intended that sections are not expanded?

HI!, do you think that it is better to expand them by default? Also, I'm trying to solve the html issue (link the html file with the css which is generated in the same folder), but not sure what it doesn't work.

bernt-matthias · 2021-01-02T19:10:48Z

Btw. is it intended that sections are not expanded?

HI!, do you think that it is better to expand them by default?

Depends. I would expand them if the intention of sections is to structure the options and hide them if they contain only advanced options.

Also, I'm trying to solve the html issue (link the html file with the css which is generated in the same folder), but not sure what it doesn't work.

What exactly is the problem. I could have a look tomorrow.

gallardoalba · 2021-01-02T19:17:45Z

Btw. is it intended that sections are not expanded?

HI!, do you think that it is better to expand them by default?

Depends. I would expand them if the intention of sections is to structure the options and hide them if they contain only advanced options.

Also, I'm trying to solve the html issue (link the html file with the css which is generated in the same folder), but not sure what it doesn't work.

What exactly is the problem. I could have a look tomorrow.

Thanks! Bjorn helped me to find the problem with the css file. About the sections, I have expanded those that I consider basics.

bernt-matthias · 2021-01-03T12:35:44Z

Excellent. Just noticed that the html output is incomplete (reported upstream here: BrendelGroup/AEGeAn#257). Since the browser still renders this nicely we can go ahead and merge this anyway .. or wait for the feedback of the author.

bgruening · 2021-01-03T12:47:13Z

@bernt-matthias your call :)

bernt-matthias · 2021-01-03T13:45:44Z

Lets wait for the fix. Seems that @gallardoalba is on it.

gallardoalba · 2021-01-03T14:22:20Z

Lets wait for the fix. Seems that @gallardoalba is on it.

Fixed. Let me know if any additional modification is necessary.

bernt-matthias · 2021-01-03T14:41:42Z

Great work @gallardoalba

gallardoalba · 2021-01-03T15:32:24Z

Great work @gallardoalba

Thank you and @bgruening for your help.

Added AEGeAN toolkit

88ca8e7

bgruening reviewed Dec 23, 2020

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gallardoalba added 6 commits December 23, 2020 23:20

Added .shed.yml file

ab4242f

Update AEGeAn toolkit

dc3ee5d

Update AEGEaN toolkit tests

d7fc79d

Update AEGEaN test files

73b4d30

Update parseval test output

f3a6035

Update parseval.xml

d6bc83f

gallardoalba changed the title ~~Added AEGeAN toolkit~~ Added AEGeAn toolkit Dec 25, 2020

bgruening reviewed Dec 26, 2020

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bernt-matthias reviewed Dec 26, 2020

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gallardoalba added 2 commits December 28, 2020 00:16

Update AEGeAn toolkit PR

ec1e649

Updated shed.yml file

edf959f

gallardoalba added 4 commits December 28, 2020 23:57

Update tests

e3e8662

Update locuspocus

b094b87

Update locuspocus tests

ad1f1eb

Update locuspocus.xml

ca15e29

bernt-matthias reviewed Dec 29, 2020

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gallardoalba added 7 commits December 29, 2020 12:04

Updated locuspocus.xml select

669673c

Updated .shed.yml

b0c1455

Updated .shed.yml fix

d40dcd3

Updated .shed.yml fix(2)

328c6a8

Update locuspocus.xml minor fixes

faa992b

Update locuspocus.xml minor fixes(2)

f9f88ec

Update test parameters

3b24bdc

bernt-matthias reviewed Dec 29, 2020

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bernt-matthias reviewed Dec 29, 2020

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gallardoalba and others added 2 commits December 29, 2020 21:33

Update tools/aegean/gaeval.xml

2b21b95

Test variable format. Co-authored-by: M Bernt <[email protected]>

Update tools/aegean/gaeval.xml

39ea989

Test variable format. Co-authored-by: M Bernt <[email protected]>

gallardoalba and others added 10 commits December 30, 2020 15:43

Update AEGeAn toolkit version_command and parameters

3581d3d

Update .shed.yml file

0a6d220

Update AEGeAn multiple inputs

0576da3

Update locuspocus test 8

113522c

Updated parseval.xml outputs

6aac58b

Update AEGeAn toolkit suggestions

21f48c2

Fix locuspocus.xml expand tag

b05c00b

Update parseval.xml css file

fcd085a

fix output files

3859099

use argument instead of name

37fed22

cont.

edba35e

Update AEGeAn replace name by argument

c69db1f

bgruening approved these changes Jan 3, 2021

View reviewed changes

Update AEGeAn html output tags

373b199

bernt-matthias merged commit e6c0151 into galaxyproject:master Jan 3, 2021

gallardoalba deleted the aegean-toolkit branch January 3, 2021 15:32

gallardoalba restored the aegean-toolkit branch January 5, 2021 19:17

gallardoalba deleted the aegean-toolkit branch January 5, 2021 19:27

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Added AEGeAn toolkit #3397

Added AEGeAn toolkit #3397

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Added AEGeAn toolkit #3397

Added AEGeAn toolkit #3397

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