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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
| author | ufz |
|---|---|
| date | Tue, 22 Jul 2025 11:09:24 +0000 |
| parents | 315c2ed31af1 |
| children |
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<tool id="phi_toolkit_report" name="PHI toolkit report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> <description></description> <icon src="logo.jpg"/> <macros> <token name="@TOOL_VERSION@">0.2.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="zenodo_collection_element" tokens="id" token_suffix=""> <element name="@ID@@SUFFIX@" location="https://zenodo.org/records/15594463/files/@ID@.fasta.fasta?download=1" value="genomes/@ID@.fasta" ftype="fasta"/> </xml> <xml name="test_collection_element" tokens="id,folder,ext,suffix"> <element name="@ID@@SUFFIX@" value="@FOLDER@/@ID@.fasta.@EXT@" ftype="@EXT@"/> </xml> <xml name="test_collection_non_empty" tokens="name,folder,ext" token_suffix=""> <param name="@NAME@"> <collection type="list"> <expand macro="test_collection_element" id="NC_000913" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_002737" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_008261" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_009012" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_014168" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_014212" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_014364" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_015761" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_017033" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_018068" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_018515" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_019936" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_021184" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <yield/> </collection> </param> </xml> <xml name="test_collection" tokens="name,folder,ext" token_suffix=""> <expand macro="test_collection_non_empty" name="@NAME@" folder="@FOLDER@" ext="@EXT@" suffix="@SUFFIX@"> <expand macro="test_collection_element" id="NC_003450" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_012982" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_014008" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_014211" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_014363" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_017095" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_018014" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_019897" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> <expand macro="test_collection_element" id="NC_019904" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/> </expand> </xml> </macros> <!-- TODO <xrefs> <xref type="bio.tools"></xref> </xrefs> --> <requirements> <requirement type="package" version="2.74.0">bioconductor-biostrings</requirement> <requirement type="package" version="1.58.0">bioconductor-genomicranges</requirement> <requirement type="package" version="1.18.0">bioconductor-gmoviz</requirement> <requirement type="package" version="0.2.1">r-formattable</requirement> <requirement type="package" version="1.0.1">r-here</requirement> <requirement type="package" version="2.2.1">r-janitor</requirement> <requirement type="package" version="1.4.0">r-kableextra</requirement> <requirement type="package" version="1.3.0">r-patchwork</requirement> <requirement type="package" version="2.0.0">r-tidyverse</requirement> <requirement type="package" version="2.0.2">r-base64</requirement> <requirement type="package" version="3.5.0">r-pdftools</requirement> </requirements> <version_command><![CDATA[ echo $(R --vanilla --slave -e 'required_packages <- c("tidyverse", "janitor", "here", "kableExtra", "gmoviz", "circlize", "GenomicRanges", "patchwork", "fs", "tools", "scales", "formattable", "pdftools", "base64"); invisible(lapply(required_packages, library, character.only = TRUE, quietly=TRUE, verbose=FALSE)); sessionInfo()' 2> /dev/null) ]]></version_command> <command detect_errors="exit_code"><![CDATA[ #import re mkdir -p data/genomes && #for e in $genomes #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) ln -s '$e' 'data/genomes/${id}.fna' && #end for mkdir -p data/host_analyses && mkdir -p data/virus_analyses && ## checkm mkdir -p data/host_analyses/checkm2 && ln -s '$checkm' data/host_analyses/checkm2/quality_report.tsv && ## defense-finder inputs mkdir -p data/host_analyses/defense-finder && #for e in $defense_finder #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/host_analyses/defense-finder/${id}/' && ln -s '$e' 'data/host_analyses/defense-finder/${id}/${id}_defense_finder_systems.tsv' && #end for ## genomad inputs mkdir -p data/host_analyses/genomad && #for e in $genomad #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' && ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus_summary.tsv' && #end for #for e in $genomad_phages #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' && ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus.fna' && #end for #for e in $genomad_annotations #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' && ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus_genes.tsv' && #end for ## GTDBTK mkdir -p data/host_analyses/gtdbtk && ln -s '$gtdb_summary' data/host_analyses/gtdbtk/gtdbtk.bac120.summary.tsv && ## CheckV mkdir -p data/virus_analyses/checkv && #for e in $checkv #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/virus_analyses/checkv/${id}/' && ln -s '$e' 'data/virus_analyses/checkv/${id}/quality_summary.tsv' && #end for ## drep compare mkdir -p data/virus_analyses/drep_compare && #for e in $drep_compare #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/virus_analyses/drep_compare/${id}/data_tables' && ln -s '$e' 'data/virus_analyses/drep_compare/${id}/data_tables/Cdb.csv' && #end for #for e in $drep_compare_clustering_dendrogram #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir 'data/virus_analyses/drep_compare/${id}/figures/' && ln -s '$e' 'data/virus_analyses/drep_compare/${id}/figures/Primary_clustering_dendrogram.pdf' && #end for ## iphop mkdir -p data/virus_analyses/iphop && #for e in $iphop #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/virus_analyses/iphop/${id}/' && ln -s '$e' 'data/virus_analyses/iphop/${id}/Host_prediction_to_genome_m90.csv' && #end for ## abricate mkdir -p data/virus_analyses/abricate && #for e in $abricate #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/virus_analyses/abricate/${id}/' && ln -s '$e' 'data/virus_analyses/abricate/${id}/${id}_virus_vfdb.tsv' && #end for ## vibrant mkdir -p data/virus_analyses/vibrant && #for e in $vibrant #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) mkdir -p 'data/virus_analyses/vibrant/${id}/VIBRANT_${id}_virus/VIBRANT_results_${id}_virus/' && ln -s '$e' 'data/virus_analyses/vibrant/${id}/VIBRANT_${id}_virus/VIBRANT_results_${id}_virus/VIBRANT_AMG_individuals_${id}_virus.tsv' && #end for Rscript -e "library(rmarkdown); render('$__tool_directory__/report.Rmd', output_dir='"\$(pwd)"', output_format = 'html_document', intermediates_dir = '"\$(pwd)"', knit_root_dir='"\$(pwd)"')" && cp report.html '$report' && >&2 echo "debug.log:" && >&2 cat debug.log ]]></command> <inputs> <param type="data_collection" name="genomes" format="fasta" label="Genomes"/> <param type="data" name="checkm" format="tabular" label="Checkm2 quality report"/> <param type="data_collection" name="genomad" format="tabular" label="geNomad Virus Summary"/> <param type="data_collection" name="genomad_phages" format="fasta" label="geNomad Virus fasta"/> <param type="data_collection" name="genomad_annotations" format="tabular" label="geNomad Virus genes"/> <param type="data_collection" name="defense_finder" format="tabular" label="DefenseFinder systems"/> <param type="data" name="gtdb_summary" format="tsv" label="GTDB-Tk summary"/> <param type="data_collection" name="checkv" format="tabular" label="CheckV Quality summary"/> <param type="data_collection" name="drep_compare" format="csv" label="drep compare Cdb.csv"/> <param type="data_collection" name="drep_compare_clustering_dendrogram" format="pdf" label="drep compare clustering dendrogram"/> <param type="data_collection" name="iphop" format="csv" label="iPHop Host prediction to genome"/> <param type="data_collection" name="abricate" format="tabular" label="Abricate results"/> <param type="data_collection" name="vibrant" format="tabular" label="Vibrant Individual predicted virus AMGs" help="Vibrant output option 'Individual predicted virus AMGs by protein and its respective genome'"/> </inputs> <outputs> <data name="report" format="html"/> </outputs> <tests> <test> <param name="genomes"> <collection type="list"> <expand macro="zenodo_collection_element" id="NC_000913"/> <expand macro="zenodo_collection_element" id="NC_002737"/> <expand macro="zenodo_collection_element" id="NC_008261"/> <expand macro="zenodo_collection_element" id="NC_009012"/> <expand macro="zenodo_collection_element" id="NC_014168"/> <expand macro="zenodo_collection_element" id="NC_014212"/> <expand macro="zenodo_collection_element" id="NC_014364"/> <expand macro="zenodo_collection_element" id="NC_015761"/> <expand macro="zenodo_collection_element" id="NC_017033"/> <expand macro="zenodo_collection_element" id="NC_018068"/> <expand macro="zenodo_collection_element" id="NC_018515"/> <expand macro="zenodo_collection_element" id="NC_019936"/> <expand macro="zenodo_collection_element" id="NC_021184"/> <expand macro="zenodo_collection_element" id="NC_003450"/> <expand macro="zenodo_collection_element" id="NC_012982"/> <expand macro="zenodo_collection_element" id="NC_014008"/> <expand macro="zenodo_collection_element" id="NC_014211"/> <expand macro="zenodo_collection_element" id="NC_014363"/> <expand macro="zenodo_collection_element" id="NC_017095"/> <expand macro="zenodo_collection_element" id="NC_018014"/> <expand macro="zenodo_collection_element" id="NC_019897"/> <expand macro="zenodo_collection_element" id="NC_019904"/> </collection> </param> <param name="checkm" value="checkm2.Quality_report.tabular"/> <expand macro="test_collection" name="genomad" folder="genomad_virus_summary" ext="tabular"/> <expand macro="test_collection" name="genomad_phages" folder="genomad_virus_fasta" ext="fasta"/> <expand macro="test_collection" name="genomad_annotations" folder="genomad_virus_genes" ext="tabular"/> <expand macro="test_collection" name="defense_finder" folder="defense_finder_systems" ext="tabular"/> <param name="gtdb_summary" value="gtdbtk.bac120.summary"/> <expand macro="test_collection_non_empty" name="checkv" folder="checkv_quality_summary" ext="tabular"/> <expand macro="test_collection_non_empty" name="drep_compare" folder="drep_compare" ext="csv"/> <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" folder="drep_compare_clustering_dendrogram" ext="pdf"/> <expand macro="test_collection_non_empty" name="iphop" folder="iphop_host_prediction_to_genome" ext="csv"/> <expand macro="test_collection_non_empty" name="abricate" folder="abricate_results" ext="tabular"/> <expand macro="test_collection_non_empty" name="vibrant" folder="vibrant_amg_individuals" ext="tabular"/> <output name="report"> <assert_contents> <has_size min="100"/> <has_line line="<html>"/> <has_text text="Error: " negate="true"/> </assert_contents> </output> </test> <!-- test with collection element identifiers contain suffix .fasta also GTDBTk and CheckM2 output tables contain the .fasta suffix--> <test> <param name="genomes"> <collection type="list"> <expand macro="zenodo_collection_element" id="NC_000913" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_002737" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_008261" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_009012" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_014168" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_014212" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_014364" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_015761" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_017033" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_018068" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_018515" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_019936" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_021184" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_003450" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_012982" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_014008" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_014211" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_014363" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_017095" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_018014" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_019897" suffix=".fasta"/> <expand macro="zenodo_collection_element" id="NC_019904" suffix=".fasta"/> </collection> </param> <param name="checkm" value="checkm2.Quality_report-wext.tabular"/> <expand macro="test_collection" name="genomad" suffix=".fasta" folder="genomad_virus_summary" ext="tabular"/> <expand macro="test_collection" name="genomad_phages" suffix=".fasta" folder="genomad_virus_fasta" ext="fasta"/> <expand macro="test_collection" name="genomad_annotations" suffix=".fasta" folder="genomad_virus_genes" ext="tabular"/> <expand macro="test_collection" name="defense_finder" suffix=".fasta" folder="defense_finder_systems" ext="tabular"/> <param name="gtdb_summary" value="gtdbtk.bac120-wext.summary"/> <expand macro="test_collection_non_empty" name="checkv" suffix=".fasta" folder="checkv_quality_summary" ext="tabular"/> <expand macro="test_collection_non_empty" name="drep_compare" suffix=".fasta" folder="drep_compare" ext="csv"/> <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" suffix=".fasta" folder="drep_compare_clustering_dendrogram" ext="pdf"/> <expand macro="test_collection_non_empty" name="iphop" suffix=".fasta" folder="iphop_host_prediction_to_genome" ext="csv"/> <!-- TODO remove from test-data <expand macro="test_collection_non_empty" name="phatyp" folder="phabox_phatyp" ext="tabular"/> --> <expand macro="test_collection_non_empty" name="abricate" suffix=".fasta" folder="abricate_results" ext="tabular"/> <expand macro="test_collection_non_empty" name="vibrant" suffix=".fasta" folder="vibrant_amg_individuals" ext="tabular"/> <output name="report"> <assert_contents> <has_size min="100"/> <has_line line="<html>"/> <has_text text="Error: " negate="true"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Create a report for the PHI toolkit workflow. Usage ..... **Input** - Genomes - Checkm2 quality report - geNomad Virus Summary - geNomad Virus genes - DefenseFinder systems - GTDB-Tk summary - CheckV Quality summary - drep compare Cdb.csv - drep compare clustering dendrogram - iPHop Host prediction to genome - Abricate results - Vibrant Individual predicted virus AMGs **Output** A html report summarizing the results. ]]></help> <!-- <citations> <citation type="doi"> </citation> </citations> --> </tool>