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Pharokka wrapper #5130

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merged 14 commits into from
Mar 1, 2023
Merged

Pharokka wrapper #5130

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1817d01
initial commit of pharokka wrapper
paulzierep Feb 14, 2023
c3e3ee4
added shed file
paulzierep Feb 14, 2023
f3303f5
added output labels
paulzierep Feb 14, 2023
6485f67
solved "pharokka --version bug", failed without error message
paulzierep Feb 15, 2023
dd6497a
* correct output created
paulzierep Feb 15, 2023
a5363f7
Thanks to the comments I did:
paulzierep Feb 15, 2023
5dbd827
* added zip as requirement
paulzierep Feb 15, 2023
724273a
Update pharokka.xml
bgruening Feb 15, 2023
174999a
Improvements:
paulzierep Feb 16, 2023
c0cdf33
Merge branch 'pharokka-wrapper' of https://github.com/paulzierep/tool…
paulzierep Feb 16, 2023
9a53e8a
tabs to spaces
paulzierep Feb 16, 2023
2ae9205
* removed option to add own DB
paulzierep Feb 16, 2023
cc3b57e
updated .loc.sample
paulzierep Feb 16, 2023
f3d0382
Improved:
paulzierep Feb 21, 2023
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11 changes: 11 additions & 0 deletions tools/pharokka/.shed.yml
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owner: iuc
name: pharokka
description: rapid standardised annotation tool for bacteriophage genomes and metagenomes
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
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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.

remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka
categories:
- Genome annotation
homepage_url: https://github.com/gbouras13/pharokka
188 changes: 188 additions & 0 deletions tools/pharokka/pharokka.xml
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<tool id='pharokka' name='bacteriophage annotation' version='1.2.0' python_template_version='3.5' profile='21.05'>
<description>
rapid standardised annotation tool for bacteriophage genomes and metagenomes
</description>
<requirements>
<requirement type='package' version='1.2.0'>
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please use macos and a TOKEN here, see https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-versions

pharokka
</requirement>
<requirement type='package' version='3.0'>
zip
</requirement>
</requirements>
<version_command>
pharokka.py --version
</version_command>
<command detect_errors='exit_code'>
<![CDATA[
## get DB based on data table or history
#if str( $reference_source.reference_source_selector ) == 'history':
echo 'use history' &&
mkdir pharokka_db &&
unzip '$reference_source.db_histroy' -d pharokka_db &&
#else:
echo 'use cache' &&
mkdir pharokka_db &&
unzip '$reference_source.db_cached.fields.path' -d pharokka_db &&
#end if

## 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 &&
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all paths and text parameter needs to be single-quoted

#else:
pharokka.py -i $fasta -o pharokka_output -d pharokka_db -t \${GALAXY_SLOTS:-8} $gene_predictor $meta -e $evalue --terminase --terminase_strand $terminase.terminase_strand --terminase_start $terminase.terminase_start &&
#end if

## create output
zip -r out.zip pharokka_output
]]>
</command>
<inputs>
<!-- the genome -->
<param type='data' name='fasta' format='fasta' help='Please upload an genome file of a bacteriophage in fasta format.' label='Bacteriophage genome'/>
<!-- the DB -->
<conditional name='reference_source'>
<param name='reference_source_selector' type='select' label='Load DB from'>
<option value='cached'>
Local cache
</option>
<option value='history'>
History
</option>
</param>
<when value='cached'>
<param name='db_cached' type='select' label='Using built-in pharokka DB' help='Using built-in pharokka DB'>
<options from_data_table='pharokka_db'>
</options>
<validator type='no_options' message='A built-in pharokka DB is not available for the build associated with the selected input file' />
</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' />
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where do users get such a DB?

</when>
</conditional>
<!-- additional arguments -->
<param name='gene_predictor' type='select' label='User specified gene predictor'>
<option value='-g phanotate'>
Phanotate
</option>
<option value='-g prodigal'>
Prodigal
</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.' />
<!-- optional arguments -->
<conditional name='terminase'>
<param name='terminase_selector' type='select' label='Runs - terminase large subunit - re-orientation mode. Single genome input only and requires --terminase_strand and --terminase_start to be specified.'>
<option value='no_terminase'>
Do not run 'terminase large subunit' re-orientation mode.
</option>
<option value='run_terminase'>
Runs 'terminase large subunit' re-orientation mode.
</option>
</param>
<when value='no_terminase'>
</when>
<when value='run_terminase'>
<param name='terminase_strand' type='select' label='Strand of terminase large subunit.'>
<option value='pos'>
Positive
</option>
<option value='neg'>
Negative
</option>
</param>
<param name='terminase_start' type='integer' value='1' label='Start coordinate of the terminase large subunit.' />
</when>
</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' />
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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.

<data name='pharokka_gbk' format='genbank' from_work_dir='pharokka_output/pharokka.gbk' label='${tool.name} on ${on_string}: Genbank' />
<data name='pharokka_gff' format='gff' from_work_dir='pharokka_output/pharokka.gff' label='${tool.name} on ${on_string}: GFF' />
</outputs>
<tests>
<!-- test input from history -->
<test>
<param name='reference_source_selector' value='history' />
<param name='db_histroy' value='subset_pharokka_db.zip' />
<param name='fasta' value='SAOMS1.fasta' />
<!-- check file size and text since output is non-deterministic -->
<output name='pharokka_gbk'>
<assert_contents>
<has_size value='353875' delta='10' />
<has_text text='VERSION MW460250_1' />
</assert_contents>
</output>
<output name='pharokka_gff'>
<assert_contents>
<has_size value='191497' delta='10' />
<has_text text='##sequence-region MW460250_1 1 140135' />
</assert_contents>
</output>
<!-- check created zip -->
<output name='archive_output'>
<assert_contents>
<has_archive_member path='.*\/pharokka\.gff' />
<has_archive_member path='.*\/pharokka\.gbk' />
<has_archive_member path='.*\/pharokka.*\.log' />
</assert_contents>
</output>
</test>
<!-- test input from DB -->
<test>
<param name='reference_source_selector' value='cached' />
<param name='db_cached' value='pharokka_db' />
<param name='fasta' value='SAOMS1.fasta' />
<!-- check file size and text since output is non-deterministic -->
<output name='pharokka_gbk'>
<assert_contents>
<has_size value='353875' delta='10' />
<has_text text='VERSION MW460250_1' />
</assert_contents>
</output>
<output name='pharokka_gff'>
<assert_contents>
<has_size value='191497' delta='10' />
<has_text text='##sequence-region MW460250_1 1 140135' />
</assert_contents>
</output>
<!-- check created zip -->
<output name='archive_output'>
<assert_contents>
<has_archive_member path='.*\/pharokka\.gff' />
<has_archive_member path='.*\/pharokka\.gbk' />
<has_archive_member path='.*\/pharokka.*\.log' />
</assert_contents>
</output>
</test>
</tests>
<help>
<![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.
]]>
</help>
<citations>
<citation type='bibtex'>
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please use type=doi here

@article{bouras_pharokka_2023,
title = {Pharokka: a fast scalable bacteriophage annotation tool},
volume = {39},
issn = {1367-4811},
shorttitle = {Pharokka},
url = {https://doi.org/10.1093/bioinformatics/btac776},
doi = {10.1093/bioinformatics/btac776},
abstract = {In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools either are not designed specifically for bacteriophages or are web- and email-based and require significant manual curation, which makes their integration into bioinformatic pipelines challenging. Pharokka was created to provide a tool that annotates bacteriophage genomes easily, rapidly and consistently with standards compliant outputs. Moreover, Pharokka requires only two lines of code to install and use and takes under 5 min to run for an average 50-kb bacteriophage genome.Pharokka is implemented in Python and is available as a bioconda package using ‘conda install -c bioconda pharokka’. The source code is available on GitHub (https://github.com/gbouras13/pharokka). Pharokka has been tested on Linux-64 and MacOSX machines and on Windows using a Linux Virtual Machine.},
number = {1},
urldate = {2023-02-14},
journal = {Bioinformatics},
author = {Bouras, George and Nepal, Roshan and Houtak, Ghais and Psaltis, Alkis James and Wormald, Peter-John and Vreugde, Sarah},
month = jan,
year = {2023},
pages = {btac776},
}
</citation>
</citations>
</tool>
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