Mercurial > repos > ufz > phabox_phavip
changeset 1:4844d9472fa6 draft default tip
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
| author | ufz |
|---|---|
| date | Wed, 16 Apr 2025 09:43:30 +0000 |
| parents | f5dba8d92cf0 |
| children | |
| files | macros.xml phavip.xml |
| diffstat | 2 files changed, 14 insertions(+), 9 deletions(-) [+] |
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--- a/macros.xml Tue Nov 12 09:32:52 2024 +0000 +++ b/macros.xml Wed Apr 16 09:43:30 2025 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.1.5</token> + <token name="@TOOL_VERSION@">2.1.11</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="citations"> <citations> @@ -44,7 +44,7 @@ <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity"/> <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins"/> <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-based coverage"/> - <!-- \-\-draw not recommended top be used according to CLI help --> + <!-- \-\-draw not recommended to be used according to CLI help --> </section> </xml> <token name="@NETWORK@"><![CDATA[ @@ -55,13 +55,15 @@ <xml name="crispr"> <section name="crispr" title="Options used to predict CRISPRs based on MAGs" help=""> - <param argument="--bfolder" type="data" format="true" optional="true" label="MAGS"/> + <param argument="--bfolder" type="data" format="fasta" optional="true" label="MAGS"/> + <param argument="--prophage" type="integer" value="1000" min="0" max="100000" label="Minimum alignment length for estimate potential prophage"/> <param argument="--cpident" type="float" value="90" min="90" max="100" label="Alignment identity for CRISPRs"/> <param argument="--ccov" type="float" value="90" min="0" max="100" label="Alignment coverage for CRISPRs"/> <param argument="--blast" type="select" label="BLAST program for CRISPRs" help="blastn-short will lead to more sensitive results but require more time to execute the program"> <option value="blastn">blastn</option> <option value="blastn-short">blastn-short</option> </param> + <param argument="--magonly" type="boolean" truevalue="--magonly Y" falsevalue="--magonly N" label="Only predicting host based on the provided MAGs" help="Default is to predict the host based on the MAGs and the reference database"/> </section> </xml> <token name="@CRISPR_PRE@"><![CDATA[ @@ -77,9 +79,11 @@ #if $crispr.bfolder --bfolder bfolder #end if + --prophage $crispr.prophage --cpident $crispr.cpident - --ccov $crispr.cpident + --ccov $crispr.ccov --blast $crispr.blast + $magonly ]]></token> <xml name="contamination"> @@ -181,6 +185,7 @@ - PhaGCNScore: the predicted score for each rank in the lineage. Each rank is separated by the ';'. - Genus: whether the contig has a genus level name ('-' means unknown). - GenusCluster: if the Genus is '-', the program will assign a genus-level grouping result: group_idx (idx = 1, 2, 3, ...) or singleton. This can be viewed as genus-level OTUs based on the average shared protein identities between sequences. +- Prokaryotic virus (Bacteriophages and Archaeal virus): Y/N ]]></token> <token name="@PHATYP_OUTPUT_DOC@"><![CDATA[ - TYPE: virulent or temperate (virus).
--- a/phavip.xml Tue Nov 12 09:32:52 2024 +0000 +++ b/phavip.xml Wed Apr 16 09:43:30 2025 +0000 @@ -28,30 +28,30 @@ <tests> <test expect_num_outputs="1"> <param name="dbdir" value="phaboxdb"/> - <param name="contigs" value="example_contigs.fa"/> + <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/> <output name="out"> <assert_contents> <has_line line="Accession	Length	Protein_num	Annotated_num	Annotation_rate"/> - <has_n_lines n="11"/> + <has_n_lines n="391"/> <has_n_columns n="5"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> <param name="dbdir" value="phaboxdb"/> - <param name="contigs" value="example_contigs.fa"/> + <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/> <param name="supp_outputs" value="gene_annotation"/> <output name="out"> <assert_contents> <has_line line="Accession	Length	Protein_num	Annotated_num	Annotation_rate"/> - <has_n_lines n="11"/> + <has_n_lines n="391"/> <has_n_columns n="5"/> </assert_contents> </output> <output name="phavip_annotation"> <assert_contents> <has_line line="Genome	ORF	Start	End	Strand	GC	Annotation	pident	coverage"/> - <has_n_lines n="171"/> + <has_n_lines n="8995"/> <has_n_columns n="9"/> </assert_contents> </output>