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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
comparison
equal deleted inserted replaced
0:315c2ed31af1 1:3a7f73d638ba
1 <tool id="phi_toolkit_report" name="PHI toolkit report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> 1 <tool id="phi_toolkit_report" name="PHI toolkit report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description></description> 2 <description></description>
3 <icon src="logo.jpg"/>
3 <macros> 4 <macros>
4 <token name="@TOOL_VERSION@">0.1.0</token> 5 <token name="@TOOL_VERSION@">0.2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">0</token>
6 7
7 <xml name="zenodo_collection_element" tokens="id"> 8 <xml name="zenodo_collection_element" tokens="id" token_suffix="">
8 <element name="@ID@" location="https://zenodo.org/records/15594463/files/NC_000913.fasta.fasta?download=1" value="genomes/@ID@.fasta.fasta" ftype="fasta"/> 9 <element name="@ID@@SUFFIX@" location="https://zenodo.org/records/15594463/files/@ID@.fasta.fasta?download=1" value="genomes/@ID@.fasta" ftype="fasta"/>
9 </xml> 10 </xml>
10 11
11 <xml name="test_collection_element" tokens="id,folder,ext"> 12 <xml name="test_collection_element" tokens="id,folder,ext,suffix">
12 <element name="@ID@" value="@FOLDER@/@ID@.fasta.@EXT@" ftype="@EXT@"/> 13 <element name="@ID@@SUFFIX@" value="@FOLDER@/@ID@.fasta.@EXT@" ftype="@EXT@"/>
13 </xml> 14 </xml>
14 <xml name="test_collection_non_empty" tokens="name,folder,ext"> 15 <xml name="test_collection_non_empty" tokens="name,folder,ext" token_suffix="">
15 <param name="@NAME@"> 16 <param name="@NAME@">
16 <collection type="list"> 17 <collection type="list">
17 <expand macro="test_collection_element" id="NC_000913" folder="@FOLDER@" ext="@EXT@"/> 18 <expand macro="test_collection_element" id="NC_000913" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
18 <expand macro="test_collection_element" id="NC_002737" folder="@FOLDER@" ext="@EXT@"/> 19 <expand macro="test_collection_element" id="NC_002737" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
19 <expand macro="test_collection_element" id="NC_008261" folder="@FOLDER@" ext="@EXT@"/> 20 <expand macro="test_collection_element" id="NC_008261" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
20 <expand macro="test_collection_element" id="NC_009012" folder="@FOLDER@" ext="@EXT@"/> 21 <expand macro="test_collection_element" id="NC_009012" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
21 <expand macro="test_collection_element" id="NC_014168" folder="@FOLDER@" ext="@EXT@"/> 22 <expand macro="test_collection_element" id="NC_014168" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
22 <expand macro="test_collection_element" id="NC_014212" folder="@FOLDER@" ext="@EXT@"/> 23 <expand macro="test_collection_element" id="NC_014212" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
23 <expand macro="test_collection_element" id="NC_014364" folder="@FOLDER@" ext="@EXT@"/> 24 <expand macro="test_collection_element" id="NC_014364" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
24 <expand macro="test_collection_element" id="NC_015761" folder="@FOLDER@" ext="@EXT@"/> 25 <expand macro="test_collection_element" id="NC_015761" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
25 <expand macro="test_collection_element" id="NC_017033" folder="@FOLDER@" ext="@EXT@"/> 26 <expand macro="test_collection_element" id="NC_017033" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
26 <expand macro="test_collection_element" id="NC_018068" folder="@FOLDER@" ext="@EXT@"/> 27 <expand macro="test_collection_element" id="NC_018068" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
27 <expand macro="test_collection_element" id="NC_018515" folder="@FOLDER@" ext="@EXT@"/> 28 <expand macro="test_collection_element" id="NC_018515" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
28 <expand macro="test_collection_element" id="NC_019936" folder="@FOLDER@" ext="@EXT@"/> 29 <expand macro="test_collection_element" id="NC_019936" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
29 <expand macro="test_collection_element" id="NC_021184" folder="@FOLDER@" ext="@EXT@"/> 30 <expand macro="test_collection_element" id="NC_021184" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
30 <yield/> 31 <yield/>
31 </collection> 32 </collection>
32 </param> 33 </param>
33 </xml> 34 </xml>
34 <xml name="test_collection" tokens="name,folder,ext"> 35 <xml name="test_collection" tokens="name,folder,ext" token_suffix="">
35 <expand macro="test_collection_non_empty" name="@NAME@" folder="@FOLDER@" ext="@EXT@"> 36 <expand macro="test_collection_non_empty" name="@NAME@" folder="@FOLDER@" ext="@EXT@" suffix="@SUFFIX@">
36 <expand macro="test_collection_element" id="NC_003450" folder="@FOLDER@" ext="@EXT@"/> 37 <expand macro="test_collection_element" id="NC_003450" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
37 <expand macro="test_collection_element" id="NC_012982" folder="@FOLDER@" ext="@EXT@"/> 38 <expand macro="test_collection_element" id="NC_012982" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
38 <expand macro="test_collection_element" id="NC_014008" folder="@FOLDER@" ext="@EXT@"/> 39 <expand macro="test_collection_element" id="NC_014008" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
39 <expand macro="test_collection_element" id="NC_014211" folder="@FOLDER@" ext="@EXT@"/> 40 <expand macro="test_collection_element" id="NC_014211" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
40 <expand macro="test_collection_element" id="NC_014363" folder="@FOLDER@" ext="@EXT@"/> 41 <expand macro="test_collection_element" id="NC_014363" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
41 <expand macro="test_collection_element" id="NC_017095" folder="@FOLDER@" ext="@EXT@"/> 42 <expand macro="test_collection_element" id="NC_017095" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
42 <expand macro="test_collection_element" id="NC_018014" folder="@FOLDER@" ext="@EXT@"/> 43 <expand macro="test_collection_element" id="NC_018014" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
43 <expand macro="test_collection_element" id="NC_019897" folder="@FOLDER@" ext="@EXT@"/> 44 <expand macro="test_collection_element" id="NC_019897" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
44 <expand macro="test_collection_element" id="NC_019904" folder="@FOLDER@" ext="@EXT@"/> 45 <expand macro="test_collection_element" id="NC_019904" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
45 </expand> 46 </expand>
46 </xml> 47 </xml>
47 48
48 </macros> 49 </macros>
49 <!-- TODO <xrefs> 50 <!-- TODO <xrefs>
60 <requirement type="package" version="1.3.0">r-patchwork</requirement> 61 <requirement type="package" version="1.3.0">r-patchwork</requirement>
61 <requirement type="package" version="2.0.0">r-tidyverse</requirement> 62 <requirement type="package" version="2.0.0">r-tidyverse</requirement>
62 <requirement type="package" version="2.0.2">r-base64</requirement> 63 <requirement type="package" version="2.0.2">r-base64</requirement>
63 <requirement type="package" version="3.5.0">r-pdftools</requirement> 64 <requirement type="package" version="3.5.0">r-pdftools</requirement>
64 </requirements> 65 </requirements>
66 <version_command><![CDATA[
67 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)
68 ]]></version_command>
65 <command detect_errors="exit_code"><![CDATA[ 69 <command detect_errors="exit_code"><![CDATA[
66 mkdir -p data/genomes && 70 #import re
71 mkdir -p data/genomes &&
67 #for e in $genomes 72 #for e in $genomes
68 ln -s '$e' 'data/genomes/${e.element_identifier}.fna' && 73 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
74 ln -s '$e' 'data/genomes/${id}.fna' &&
69 #end for 75 #end for
70 76
71 mkdir -p data/host_analyses && 77 mkdir -p data/host_analyses &&
72 mkdir -p data/virus_analyses && 78 mkdir -p data/virus_analyses &&
73 79
76 ln -s '$checkm' data/host_analyses/checkm2/quality_report.tsv && 82 ln -s '$checkm' data/host_analyses/checkm2/quality_report.tsv &&
77 83
78 ## defense-finder inputs 84 ## defense-finder inputs
79 mkdir -p data/host_analyses/defense-finder && 85 mkdir -p data/host_analyses/defense-finder &&
80 #for e in $defense_finder 86 #for e in $defense_finder
81 mkdir -p 'data/host_analyses/defense-finder/${e.element_identifier}/' && 87 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
82 ln -s '$e' 'data/host_analyses/defense-finder/${e.element_identifier}/${e.element_identifier}_defense_finder_systems.tsv' && 88 mkdir -p 'data/host_analyses/defense-finder/${id}/' &&
89 ln -s '$e' 'data/host_analyses/defense-finder/${id}/${id}_defense_finder_systems.tsv' &&
83 #end for 90 #end for
84 91
85 ## genomad inputs 92 ## genomad inputs
86 mkdir -p data/host_analyses/genomad && 93 mkdir -p data/host_analyses/genomad &&
87 #for e in $genomad 94 #for e in $genomad
88 mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' && 95 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
89 ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus_summary.tsv' && 96 mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' &&
97 ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus_summary.tsv' &&
90 #end for 98 #end for
91 #for e in $genomad_phages 99 #for e in $genomad_phages
92 mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' && 100 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
93 ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus.fna' && 101 mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' &&
102 ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus.fna' &&
94 #end for 103 #end for
95 #for e in $genomad_annotations 104 #for e in $genomad_annotations
96 mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' && 105 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
97 ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus_genes.tsv' && 106 mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' &&
107 ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus_genes.tsv' &&
98 #end for 108 #end for
99 109
100 ## GTDBTK 110 ## GTDBTK
101 mkdir -p data/host_analyses/gtdbtk && 111 mkdir -p data/host_analyses/gtdbtk &&
102 ln -s '$gtdb_summary' data/host_analyses/gtdbtk/gtdbtk.bac120.summary.tsv && 112 ln -s '$gtdb_summary' data/host_analyses/gtdbtk/gtdbtk.bac120.summary.tsv &&
103 113
104 ## CheckV 114 ## CheckV
105 mkdir -p data/virus_analyses/checkv && 115 mkdir -p data/virus_analyses/checkv &&
106 #for e in $checkv 116 #for e in $checkv
107 mkdir -p 'data/virus_analyses/checkv/${e.element_identifier}/' && 117 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
108 ln -s '$e' 'data/virus_analyses/checkv/${e.element_identifier}/quality_summary.tsv' && 118 mkdir -p 'data/virus_analyses/checkv/${id}/' &&
119 ln -s '$e' 'data/virus_analyses/checkv/${id}/quality_summary.tsv' &&
109 #end for 120 #end for
110 121
111 ## drep compare 122 ## drep compare
112 mkdir -p data/virus_analyses/drep_compare && 123 mkdir -p data/virus_analyses/drep_compare &&
113 #for e in $drep_compare 124 #for e in $drep_compare
114 mkdir -p 'data/virus_analyses/drep_compare/${e.element_identifier}/data_tables' && 125 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
115 ln -s '$e' 'data/virus_analyses/drep_compare/${e.element_identifier}/data_tables/Cdb.csv' && 126 mkdir -p 'data/virus_analyses/drep_compare/${id}/data_tables' &&
127 ln -s '$e' 'data/virus_analyses/drep_compare/${id}/data_tables/Cdb.csv' &&
116 #end for 128 #end for
117 #for e in $drep_compare_clustering_dendrogram 129 #for e in $drep_compare_clustering_dendrogram
118 mkdir 'data/virus_analyses/drep_compare/${e.element_identifier}/figures/' && 130 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
119 ln -s '$e' 'data/virus_analyses/drep_compare/${e.element_identifier}/figures/Primary_clustering_dendrogram.pdf' && 131 mkdir 'data/virus_analyses/drep_compare/${id}/figures/' &&
132 ln -s '$e' 'data/virus_analyses/drep_compare/${id}/figures/Primary_clustering_dendrogram.pdf' &&
120 #end for 133 #end for
121 134
122 ## iphop 135 ## iphop
123 mkdir -p data/virus_analyses/iphop && 136 mkdir -p data/virus_analyses/iphop &&
124 #for e in $iphop 137 #for e in $iphop
125 mkdir -p 'data/virus_analyses/iphop/${e.element_identifier}/' && 138 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
126 ln -s '$e' 'data/virus_analyses/iphop/${e.element_identifier}/Host_prediction_to_genome_m90.csv' && 139 mkdir -p 'data/virus_analyses/iphop/${id}/' &&
140 ln -s '$e' 'data/virus_analyses/iphop/${id}/Host_prediction_to_genome_m90.csv' &&
127 #end for 141 #end for
128 142
129 ## abricate 143 ## abricate
130 mkdir -p data/virus_analyses/abricate && 144 mkdir -p data/virus_analyses/abricate &&
131 #for e in $abricate 145 #for e in $abricate
132 mkdir -p 'data/virus_analyses/abricate/${e.element_identifier}/' && 146 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
133 ln -s '$e' 'data/virus_analyses/abricate/${e.element_identifier}/${e.element_identifier}_virus_vfdb.tsv' && 147 mkdir -p 'data/virus_analyses/abricate/${id}/' &&
148 ln -s '$e' 'data/virus_analyses/abricate/${id}/${id}_virus_vfdb.tsv' &&
134 #end for 149 #end for
135 150
136 ## vibrant 151 ## vibrant
137 mkdir -p data/virus_analyses/vibrant && 152 mkdir -p data/virus_analyses/vibrant &&
138 #for e in $vibrant 153 #for e in $vibrant
139 mkdir -p 'data/virus_analyses/vibrant/${e.element_identifier}/VIBRANT_${e.element_identifier}_virus/VIBRANT_results_${e.element_identifier}_virus/' && 154 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
140 ln -s '$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' && 155 mkdir -p 'data/virus_analyses/vibrant/${id}/VIBRANT_${id}_virus/VIBRANT_results_${id}_virus/' &&
156 ln -s '$e' 'data/virus_analyses/vibrant/${id}/VIBRANT_${id}_virus/VIBRANT_results_${id}_virus/VIBRANT_AMG_individuals_${id}_virus.tsv' &&
141 #end for 157 #end for
142 158
143 Rscript -e "library(rmarkdown); render('$__tool_directory__/report.Rmd', output_dir='"\$(pwd)"', output_format = 'html_document', intermediates_dir = '"\$(pwd)"', knit_root_dir='"\$(pwd)"')" && 159 Rscript -e "library(rmarkdown); render('$__tool_directory__/report.Rmd', output_dir='"\$(pwd)"', output_format = 'html_document', intermediates_dir = '"\$(pwd)"', knit_root_dir='"\$(pwd)"')" &&
144 cp report.html '$report' 160 cp report.html '$report'
161 && >&2 echo "debug.log:"
162 && >&2 cat debug.log
145 ]]></command> 163 ]]></command>
146 <inputs> 164 <inputs>
147 <param type="data_collection" name="genomes" format="fasta" label="Genomes"/> 165 <param type="data_collection" name="genomes" format="fasta" label="Genomes"/>
148 <param type="data" name="checkm" format="tabular" label="Checkm2 quality report"/> 166 <param type="data" name="checkm" format="tabular" label="Checkm2 quality report"/>
149 <param type="data_collection" name="genomad" format="tabular" label="geNomad Virus Summary"/> 167 <param type="data_collection" name="genomad" format="tabular" label="geNomad Virus Summary"/>
161 <outputs> 179 <outputs>
162 <data name="report" format="html"/> 180 <data name="report" format="html"/>
163 </outputs> 181 </outputs>
164 <tests> 182 <tests>
165 <test> 183 <test>
166 <!-- <expand macro="test_collection" name="genomes" folder="genomes" ext="fasta"/> -->
167 <param name="genomes"> 184 <param name="genomes">
168 <collection type="list"> 185 <collection type="list">
169 <expand macro="zenodo_collection_element" id="NC_000913"/> 186 <expand macro="zenodo_collection_element" id="NC_000913"/>
170 <expand macro="zenodo_collection_element" id="NC_002737"/> 187 <expand macro="zenodo_collection_element" id="NC_002737"/>
171 <expand macro="zenodo_collection_element" id="NC_008261"/> 188 <expand macro="zenodo_collection_element" id="NC_008261"/>
198 <param name="gtdb_summary" value="gtdbtk.bac120.summary"/> 215 <param name="gtdb_summary" value="gtdbtk.bac120.summary"/>
199 <expand macro="test_collection_non_empty" name="checkv" folder="checkv_quality_summary" ext="tabular"/> 216 <expand macro="test_collection_non_empty" name="checkv" folder="checkv_quality_summary" ext="tabular"/>
200 <expand macro="test_collection_non_empty" name="drep_compare" folder="drep_compare" ext="csv"/> 217 <expand macro="test_collection_non_empty" name="drep_compare" folder="drep_compare" ext="csv"/>
201 <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" folder="drep_compare_clustering_dendrogram" ext="pdf"/> 218 <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" folder="drep_compare_clustering_dendrogram" ext="pdf"/>
202 <expand macro="test_collection_non_empty" name="iphop" folder="iphop_host_prediction_to_genome" ext="csv"/> 219 <expand macro="test_collection_non_empty" name="iphop" folder="iphop_host_prediction_to_genome" ext="csv"/>
203 <!-- TODO remove from test-data <expand macro="test_collection_non_empty" name="phatyp" folder="phabox_phatyp" ext="tabular"/> -->
204 <expand macro="test_collection_non_empty" name="abricate" folder="abricate_results" ext="tabular"/> 220 <expand macro="test_collection_non_empty" name="abricate" folder="abricate_results" ext="tabular"/>
205 <expand macro="test_collection_non_empty" name="vibrant" folder="vibrant_amg_individuals" ext="tabular"/> 221 <expand macro="test_collection_non_empty" name="vibrant" folder="vibrant_amg_individuals" ext="tabular"/>
206 <output name="report"> 222 <output name="report">
207 <assert_contents> 223 <assert_contents>
208 <has_size min="100"/> 224 <has_size min="100"/>
209 <has_line line="&lt;html&gt;"/> 225 <has_line line="&lt;html&gt;"/>
226 <has_text text="Error: " negate="true"/>
227 </assert_contents>
228 </output>
229 </test>
230
231 <!-- test with collection element identifiers contain suffix .fasta
232 also GTDBTk and CheckM2 output tables contain the .fasta suffix-->
233 <test>
234 <param name="genomes">
235 <collection type="list">
236 <expand macro="zenodo_collection_element" id="NC_000913" suffix=".fasta"/>
237 <expand macro="zenodo_collection_element" id="NC_002737" suffix=".fasta"/>
238 <expand macro="zenodo_collection_element" id="NC_008261" suffix=".fasta"/>
239 <expand macro="zenodo_collection_element" id="NC_009012" suffix=".fasta"/>
240 <expand macro="zenodo_collection_element" id="NC_014168" suffix=".fasta"/>
241 <expand macro="zenodo_collection_element" id="NC_014212" suffix=".fasta"/>
242 <expand macro="zenodo_collection_element" id="NC_014364" suffix=".fasta"/>
243 <expand macro="zenodo_collection_element" id="NC_015761" suffix=".fasta"/>
244 <expand macro="zenodo_collection_element" id="NC_017033" suffix=".fasta"/>
245 <expand macro="zenodo_collection_element" id="NC_018068" suffix=".fasta"/>
246 <expand macro="zenodo_collection_element" id="NC_018515" suffix=".fasta"/>
247 <expand macro="zenodo_collection_element" id="NC_019936" suffix=".fasta"/>
248 <expand macro="zenodo_collection_element" id="NC_021184" suffix=".fasta"/>
249 <expand macro="zenodo_collection_element" id="NC_003450" suffix=".fasta"/>
250 <expand macro="zenodo_collection_element" id="NC_012982" suffix=".fasta"/>
251 <expand macro="zenodo_collection_element" id="NC_014008" suffix=".fasta"/>
252 <expand macro="zenodo_collection_element" id="NC_014211" suffix=".fasta"/>
253 <expand macro="zenodo_collection_element" id="NC_014363" suffix=".fasta"/>
254 <expand macro="zenodo_collection_element" id="NC_017095" suffix=".fasta"/>
255 <expand macro="zenodo_collection_element" id="NC_018014" suffix=".fasta"/>
256 <expand macro="zenodo_collection_element" id="NC_019897" suffix=".fasta"/>
257 <expand macro="zenodo_collection_element" id="NC_019904" suffix=".fasta"/>
258 </collection>
259 </param>
260 <param name="checkm" value="checkm2.Quality_report-wext.tabular"/>
261 <expand macro="test_collection" name="genomad" suffix=".fasta" folder="genomad_virus_summary" ext="tabular"/>
262 <expand macro="test_collection" name="genomad_phages" suffix=".fasta" folder="genomad_virus_fasta" ext="fasta"/>
263 <expand macro="test_collection" name="genomad_annotations" suffix=".fasta" folder="genomad_virus_genes" ext="tabular"/>
264 <expand macro="test_collection" name="defense_finder" suffix=".fasta" folder="defense_finder_systems" ext="tabular"/>
265 <param name="gtdb_summary" value="gtdbtk.bac120-wext.summary"/>
266 <expand macro="test_collection_non_empty" name="checkv" suffix=".fasta" folder="checkv_quality_summary" ext="tabular"/>
267 <expand macro="test_collection_non_empty" name="drep_compare" suffix=".fasta" folder="drep_compare" ext="csv"/>
268 <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" suffix=".fasta" folder="drep_compare_clustering_dendrogram" ext="pdf"/>
269 <expand macro="test_collection_non_empty" name="iphop" suffix=".fasta" folder="iphop_host_prediction_to_genome" ext="csv"/>
270 <!-- TODO remove from test-data <expand macro="test_collection_non_empty" name="phatyp" folder="phabox_phatyp" ext="tabular"/> -->
271 <expand macro="test_collection_non_empty" name="abricate" suffix=".fasta" folder="abricate_results" ext="tabular"/>
272 <expand macro="test_collection_non_empty" name="vibrant" suffix=".fasta" folder="vibrant_amg_individuals" ext="tabular"/>
273 <output name="report">
274 <assert_contents>
275 <has_size min="100"/>
276 <has_line line="&lt;html&gt;"/>
277 <has_text text="Error: " negate="true"/>
210 </assert_contents> 278 </assert_contents>
211 </output> 279 </output>
212 </test> 280 </test>
213 </tests> 281 </tests>
214 <help><![CDATA[ 282 <help><![CDATA[