Pharokka wrapper #5130
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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 | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka | ||
| categories: | ||
| - Genome annotation | ||
| homepage_url: https://github.com/gbouras13/pharokka | ||
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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"> | ||
| pharokka | ||
| </requirement> | ||
| </requirements> | ||
| <version_command> | ||
| pharokka -version | ||
| </version_command> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
| ## get DB based on data table or history | ||
| #if str( $reference_source.reference_source_selector ) == "history": | ||
| echo "use history" && | ||
| mkdir pharokka_db && | ||
| tar -xvf "$reference_source.db_histroy" --strip 1 -C pharokka_db && | ||
| #else: | ||
| echo "use cache" && | ||
| mkdir pharokka_db && | ||
| tar -xvf "$reference_source.db_cached.fields.path" --strip 1 -C pharokka_db && | ||
|
There was a problem hiding this comment. please use everywhere single-quotes, see here: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#command-formatting |
||
| #end if | ||
|
|
||
| ## 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 && | ||
|
There was a problem hiding this comment. single-quote all data params and text params There was a problem hiding this comment. Is -t 8 the number of cores? if so please use GALAXY_SLOTS |
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| #else: | ||
| pharokka.py -i $fasta -o pharokka_output -d pharokka_db -t 8 $gene_predictor $meta -e $evalue --terminase --terminase_strand $terminase.terminase_strand --terminase_start $terminase.terminase_start && | ||
| #end if | ||
|
|
||
| ## create output | ||
| zip -r out.zip pharokka_db && | ||
| cp out.zip "$archive_output" && | ||
| cp pharokka_output/pharokka.gbk "$pharokka_gbk" && | ||
|
There was a problem hiding this comment. instead of copy, you can use |
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| cp pharokka_output/pharokka.gff "$pharokka_gff" | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <!-- the genome --> | ||
| <param type="data" name="fasta" format="data" /> | ||
|
There was a problem hiding this comment. Please add a title here and maybe some help to assist the user There was a problem hiding this comment. With title, do you mean using a label tag ? |
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| <!-- 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="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" /> | ||
|
There was a problem hiding this comment. format is wrong, or needs to be specified |
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| </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" label="${tool.name} on ${on_string}: zip of the complete output" /> | ||
| <data name="pharokka_gbk" format="genbank" label="${tool.name} on ${on_string}: Genbank" /> | ||
| <data name="pharokka_gff" format="gff" label="${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.tar.gz" /> | ||
| <param name="fasta" value="SAOMS1.fasta" /> | ||
| <!-- check file size since output is non-deterministic --> | ||
| <output name="pharokka_gbk"> | ||
| <assert_contents> | ||
| <has_size value="353875" delta="300" /> | ||
|
There was a problem hiding this comment. has_size is the worst test you can do as it is very unspecific, you could use other more specific asserts if you like |
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| </assert_contents> | ||
| </output> | ||
| <output name="pharokka_gff"> | ||
| <assert_contents> | ||
| <has_size value="191497" delta="300" /> | ||
| </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 since output is non-deterministic --> | ||
| <output name="pharokka_gbk"> | ||
| <assert_contents> | ||
| <has_size value="353875" delta="300" /> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="pharokka_gff"> | ||
| <assert_contents> | ||
| <has_size value="191497" delta="300" /> | ||
| </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"> | ||
|
There was a problem hiding this comment. Please use a doi style citation https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-citations-citation There was a problem hiding this comment. That was addressed, github for some reason does not show it 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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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.