Pharokka wrapper #5130

paulzierep · 2023-02-14T14:38:15Z

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)

Had initial problems with testing the data table. But the maintainer provided a tiny version of the DB and the tests passed. Tests are only written for the main output.

bgruening · 2023-02-14T17:21:07Z

tools/pharokka/pharokka.xml

+			<!-- check file size since output is non-deterministic -->
+			<output name="pharokka_gbk">
+				<assert_contents>
+					<has_size value="353875" delta="300" />


has_size is the worst test you can do as it is very unspecific, you could use other more specific asserts if you like

bgruening · 2023-02-14T17:22:31Z

tools/pharokka/pharokka.xml

+		#else:
+		echo "use cache" &&
+		mkdir pharokka_db &&
+		tar -xvf "$reference_source.db_cached.fields.path" --strip 1 -C pharokka_db &&


please use everywhere single-quotes, see here: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#command-formatting

bgruening · 2023-02-14T17:22:54Z

tools/pharokka/pharokka.xml

+
+		## run tool
+		#if str( $terminase.terminase_selector ) == "no_terminase":
+		pharokka.py -i $fasta -o pharokka_output -d pharokka_db -t 8 $gene_predictor $meta -e $evalue &&


single-quote all data params and text params

Is -t 8 the number of cores? if so please use GALAXY_SLOTS

bgruening · 2023-02-14T17:23:42Z

tools/pharokka/pharokka.xml

+		## create output
+		zip -r out.zip pharokka_db &&
+		cp out.zip "$archive_output" &&
+		cp pharokka_output/pharokka.gbk "$pharokka_gbk" &&


instead of copy, you can use from_work_dir= in the output section

bgruening · 2023-02-14T17:24:17Z

tools/pharokka/pharokka.xml

+	</command>
+	<inputs>
+		<!-- the genome -->
+		<param type="data" name="fasta" format="data" />


Please add a title here and maybe some help to assist the user

With title, do you mean using a label tag ?

bgruening · 2023-02-14T17:25:32Z

tools/pharokka/pharokka.xml

+				</param>
+			</when>
+			<when value="history">
+				<param name="db_histroy" type="data" format="data" label="Use the folloing pharokka DB" help="You can upload a pharokka DB as tar.gz to the history and use it as DB" />


format is wrong, or needs to be specified

* improved tests * added archive test

* single quotes changed * zip as test data * improved tests * GALAXY_SLOTS * using from_work_dir=

bgruening

please see if you can add a bio.tools ID

bgruening · 2023-02-15T22:18:56Z

tools/pharokka/pharokka.xml

+		rapid standardised annotation tool for bacteriophage genomes and metagenomes
+	</description>
+	<requirements>
+		<requirement type='package' version='1.2.0'>


please use macos and a TOKEN here, see https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-versions

bgruening · 2023-02-15T22:19:20Z

tools/pharokka/pharokka.xml

+
+		## run tool
+		#if str( $terminase.terminase_selector ) == 'no_terminase':
+		pharokka.py -i $fasta -o pharokka_output -d pharokka_db -t \${GALAXY_SLOTS:-8} $gene_predictor $meta -e $evalue &&


all paths and text parameter needs to be single-quoted

bgruening · 2023-02-15T22:19:53Z

tools/pharokka/pharokka.xml

+		]]>
+	</help>
+	<citations>
+		<citation type='bibtex'>


please use type=doi here

bgruening · 2023-02-15T22:20:32Z

tools/pharokka/pharokka.xml

+				</param>
+			</when>
+			<when value='history'>
+				<param name='db_histroy' type='data' format='zip' label='Use the folloing pharokka DB' help='You can upload a pharokka DB as zip to the history and use it as DB' />


where do users get such a DB?

bgruening · 2023-02-15T22:22:45Z

tools/pharokka/pharokka.xml

+		</conditional>
+	</inputs>
+	<outputs>
+		<data name='archive_output' format='zip' from_work_dir='out.zip' label='${tool.name} on ${on_string}: zip of the complete output' />


can we make this output file optional, so that the user needs to select an option to output it ... I don't think its so useful by default.

* optional zip output * DB source * single-quotes in cheetah * citation doi * macros and tokens * bio tools ID

…s-iuc into pharokka-wrapper

* added test DB as folder

bgruening · 2023-02-16T21:19:29Z

tools/pharokka/pharokka.xml

+        <![CDATA[
+        pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
+
+        If you are looking for rapid standardised annotation of bacterial genomes, please use prokka, which inspired the creation of pharokka, or bakta.


bakta should be used today, so I guess its save to recommend bakta.
This help could be enhanced a bit and more information be given?

bgruening · 2023-02-16T21:20:57Z

tools/pharokka/pharokka.xml

+            </option>
+        </param>
+        <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="meta mode for metavirome input samples" />
+        <param name="evalue" type="integer" value="100000" label="E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05." />


please use min and max value whenever you can for floats and ints. the value looks for an evalue strange.

I changed it, but the values go from 1e-20 to 10, however the bar does not really allow choosing something like 1e-10 ... I think it would be a good feature if a log scale could be used...

But max 10 you can add correct?

bgruening · 2023-02-16T21:21:40Z

tools/pharokka/pharokka.xml

+        ## create output
+        #if $zip_output == 'true':
+            zip -r out.zip pharokka_output
+        #else:


this else should not be needed

bgruening · 2023-02-16T21:23:07Z

tools/pharokka/pharokka.xml

+    <command detect_errors="exit_code">
+        <![CDATA[
+        ## run tool
+        #if str( $terminase.terminase_selector ) == 'no_terminase':


isn't there a else case missing for run_terminase?

bgruening · 2023-02-16T21:24:04Z

tools/pharokka/.shed.yml

+long_description: |
+  pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 
+  If you are looking for rapid standardised annotation of bacterial genomes, please use prokka, 
+  which inspired the creation of pharokka, or bakta. Repository-Maintainer: Paul Zierep


You can get credits by adding tags to the tools ... see https://docs.galaxyproject.org/en/latest/dev/schema.html

And add yourself as maintainer via the codeowner file in this repo.

bgruening · 2023-02-16T21:24:31Z

tools/pharokka/pharokka.xml

@@ -0,0 +1,154 @@
+<tool id="pharokka" name="bacteriophage annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.7" profile="@PROFILE@">


please remove the python_template_version its not needed.

* help * credits * min/max parameter * else in code

bernt-matthias · 2023-02-26T07:45:57Z

tools/pharokka/pharokka.xml

+		]]>
+	</help>
+	<citations>
+		<citation type="bibtex">


Please use a doi style citation https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-citations-citation

That was addressed, github for some reason does not show it here.

bgruening · 2023-03-01T22:22:32Z

Thanks @paulzierep

gxydevbot · 2023-03-01T22:35:27Z

Attention: deployment skipped!

https://github.com/galaxyproject/tools-iuc/actions/runs/4308502357

bernt-matthias · 2023-03-02T09:09:04Z

Due to test failures. Will restart .. lets see

gxydevbot · 2023-03-02T09:15:46Z

Attention: deployment skipped!

https://github.com/galaxyproject/tools-iuc/actions/runs/4308502357

bernt-matthias · 2023-03-02T09:19:18Z

Still fails with exit code 1

bernt-matthias · 2023-03-02T11:47:23Z

Traceback (most recent call last):
  File "/usr/local/bin/pharokka.py", line 5, in <module>
    import processes
  File "/usr/local/bin/processes.py", line 8, in <module>
    from BCBio import GFF
  File "/usr/local/lib/python3.10/site-packages/BCBio/GFF/__init__.py", line 3, in <module>
    from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple
  File "/usr/local/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 34, in <module>
    from Bio.Seq import UnknownSeq
ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq' (/usr/local/lib/python3.10/site-packages/Bio/Seq.py)

https://github.com/biopython/biopython/blob/dcf52bd4546410e1a60d39fbcd4c0041ec1e6fe6/DEPRECATED.rst#biosequnknownseq

So it seems that in biopython bcbio-gff should pin biopython to <=1.79 .. then we can bump the multipackage container and we are fine.

Could you do this @paulzierep? .. maybe also ask the pharokka developers why they use an extra gff module .. biopython itself should have a gff parser

abretaud · 2023-03-02T12:51:22Z

For the record, the error in bcbio-gff is tracked there (there's a pending PR)

paulzierep · 2023-03-02T13:05:36Z

I guess that can be solved by updating to v1.2.1 gbouras13/pharokka#238

…5130)

bernt-matthias · 2023-03-02T14:04:54Z

I guess that can be solved by updating to v1.2.1

Think so. Could you prepare a PR for the IUC repo?

Note, I also added the biopython pin to bcbio-gff: bioconda/bioconda-recipes#39703

bernt-matthias · 2023-03-02T14:06:01Z

Ahh. you already did :)

Still wondering why our CI did not catch this problem before merging ...

paulzierep added 3 commits February 14, 2023 15:31

initial commit of pharokka wrapper

1817d01

added shed file

c3e3ee4

added output labels

f3303f5

bgruening reviewed Feb 14, 2023

View reviewed changes

paulzierep added 4 commits February 15, 2023 08:42

solved "pharokka --version bug", failed without error message

6485f67

* correct output created

dd6497a

* improved tests * added archive test

Thanks to the comments I did:

a5363f7

* single quotes changed * zip as test data * improved tests * GALAXY_SLOTS * using from_work_dir=

* added zip as requirement

5dbd827

paulzierep requested a review from bgruening February 15, 2023 15:22

Update pharokka.xml

724273a

bgruening reviewed Feb 15, 2023

View reviewed changes

paulzierep added 2 commits February 16, 2023 10:51

Improvements:

174999a

* optional zip output * DB source * single-quotes in cheetah * citation doi * macros and tokens * bio tools ID

Merge branch 'pharokka-wrapper' of https://github.com/paulzierep/tool…

c0cdf33

…s-iuc into pharokka-wrapper

paulzierep requested a review from bgruening February 16, 2023 10:16

paulzierep added 3 commits February 16, 2023 11:50

tabs to spaces

9a53e8a

* removed option to add own DB

2ae9205

* added test DB as folder

updated .loc.sample

cc3b57e

bgruening reviewed Feb 16, 2023

View reviewed changes

Improved:

f3d0382

* help * credits * min/max parameter * else in code

paulzierep requested a review from bgruening February 21, 2023 13:18

bernt-matthias reviewed Feb 26, 2023

View reviewed changes

bgruening approved these changes Mar 1, 2023

View reviewed changes

bgruening merged commit b5b9d62 into galaxyproject:main Mar 1, 2023

paulzierep added a commit to paulzierep/tools-iuc that referenced this pull request Mar 2, 2023

update version to 1.2.1 fixes bcbio-gff biopython bug (galaxyproject#…

9d3ce70

…5130)

paulzierep mentioned this pull request Mar 2, 2023

Update pharokka version to 1.2.1 fixes bcbio-gff biopython bug (#5130) #5169

Merged

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bernt-matthias pushed a commit that referenced this pull request Mar 2, 2023

update version to 1.2.1 fixes bcbio-gff biopython bug (#5130) (#5169)

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Pharokka wrapper #5130

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		@@ -0,0 +1,154 @@
		<tool id="pharokka" name="bacteriophage annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.7" profile="@PROFILE@">

Pharokka wrapper #5130

Pharokka wrapper #5130

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