Mercurial > repos > ufz > phi_toolkit_report
diff phitk.xml @ 1:3a7f73d638ba draft default tip
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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--- a/phitk.xml Wed Jun 04 17:36:40 2025 +0000 +++ b/phitk.xml Tue Jul 22 11:09:24 2025 +0000 @@ -1,47 +1,48 @@ <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@">0.1.0</token> + <token name="@TOOL_VERSION@">0.2.0</token> <token name="@VERSION_SUFFIX@">0</token> - <xml name="zenodo_collection_element" tokens="id"> - <element name="@ID@" location="https://zenodo.org/records/15594463/files/NC_000913.fasta.fasta?download=1" value="genomes/@ID@.fasta.fasta" ftype="fasta"/> + <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"> - <element name="@ID@" value="@FOLDER@/@ID@.fasta.@EXT@" ftype="@EXT@"/> + <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"> + <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" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_002737" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_008261" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_009012" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_014168" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_014212" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_014364" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_015761" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_017033" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_018068" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_018515" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_019936" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_021184" folder="@FOLDER@" ext="@EXT@"/> + <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"> - <expand macro="test_collection_non_empty" name="@NAME@" folder="@FOLDER@" ext="@EXT@"> - <expand macro="test_collection_element" id="NC_003450" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_012982" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_014008" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_014211" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_014363" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_017095" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_018014" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_019897" folder="@FOLDER@" ext="@EXT@"/> - <expand macro="test_collection_element" id="NC_019904" folder="@FOLDER@" ext="@EXT@"/> + <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> @@ -62,10 +63,15 @@ <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[ - mkdir -p data/genomes && + #import re + mkdir -p data/genomes && #for e in $genomes - ln -s '$e' 'data/genomes/${e.element_identifier}.fna' && + #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier) + ln -s '$e' 'data/genomes/${id}.fna' && #end for mkdir -p data/host_analyses && @@ -78,23 +84,27 @@ ## defense-finder inputs mkdir -p data/host_analyses/defense-finder && #for e in $defense_finder - mkdir -p 'data/host_analyses/defense-finder/${e.element_identifier}/' && - ln -s '$e' 'data/host_analyses/defense-finder/${e.element_identifier}/${e.element_identifier}_defense_finder_systems.tsv' && + #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 $genomad - mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' && - ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus_summary.tsv' && + #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 $genomad_phages - mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' && - ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus.fna' && + #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 $genomad_annotations - mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' && - ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus_genes.tsv' && + #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 @@ -104,44 +114,52 @@ ## CheckV mkdir -p data/virus_analyses/checkv && #for e in $checkv - mkdir -p 'data/virus_analyses/checkv/${e.element_identifier}/' && - ln -s '$e' 'data/virus_analyses/checkv/${e.element_identifier}/quality_summary.tsv' && + #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 $drep_compare - mkdir -p 'data/virus_analyses/drep_compare/${e.element_identifier}/data_tables' && - ln -s '$e' 'data/virus_analyses/drep_compare/${e.element_identifier}/data_tables/Cdb.csv' && + #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 $drep_compare_clustering_dendrogram - mkdir 'data/virus_analyses/drep_compare/${e.element_identifier}/figures/' && - ln -s '$e' 'data/virus_analyses/drep_compare/${e.element_identifier}/figures/Primary_clustering_dendrogram.pdf' && + #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 $iphop - mkdir -p 'data/virus_analyses/iphop/${e.element_identifier}/' && - ln -s '$e' 'data/virus_analyses/iphop/${e.element_identifier}/Host_prediction_to_genome_m90.csv' && + #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 $abricate - mkdir -p 'data/virus_analyses/abricate/${e.element_identifier}/' && - ln -s '$e' 'data/virus_analyses/abricate/${e.element_identifier}/${e.element_identifier}_virus_vfdb.tsv' && + #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 $vibrant - mkdir -p 'data/virus_analyses/vibrant/${e.element_identifier}/VIBRANT_${e.element_identifier}_virus/VIBRANT_results_${e.element_identifier}_virus/' && - ln -s '$e' 'data/virus_analyses/vibrant/${e.element_identifier}/VIBRANT_${e.element_identifier}_virus/VIBRANT_results_${e.element_identifier}_virus/VIBRANT_AMG_individuals_${e.element_identifier}_virus.tsv' && + #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"/> @@ -163,7 +181,6 @@ </outputs> <tests> <test> - <!-- <expand macro="test_collection" name="genomes" folder="genomes" ext="fasta"/> --> <param name="genomes"> <collection type="list"> <expand macro="zenodo_collection_element" id="NC_000913"/> @@ -200,13 +217,64 @@ <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"/> - <!-- 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" 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> @@ -244,4 +312,4 @@ <!-- <citations> <citation type="doi"> </citation> </citations> --> -</tool> \ No newline at end of file +</tool>