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comparison phitk.xml @ 0:315c2ed31af1 draft

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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
author ufz
date Wed, 04 Jun 2025 17:36:40 +0000
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children 3a7f73d638ba
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-1:000000000000 0:315c2ed31af1
1 <tool id="phi_toolkit_report" name="PHI toolkit report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description></description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6
7 <xml name="zenodo_collection_element" tokens="id">
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 </xml>
10
11 <xml name="test_collection_element" tokens="id,folder,ext">
12 <element name="@ID@" value="@FOLDER@/@ID@.fasta.@EXT@" ftype="@EXT@"/>
13 </xml>
14 <xml name="test_collection_non_empty" tokens="name,folder,ext">
15 <param name="@NAME@">
16 <collection type="list">
17 <expand macro="test_collection_element" id="NC_000913" 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_008261" 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_014168" 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_014364" 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_017033" 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_018515" 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_021184" folder="@FOLDER@" ext="@EXT@"/>
30 <yield/>
31 </collection>
32 </param>
33 </xml>
34 <xml name="test_collection" tokens="name,folder,ext">
35 <expand macro="test_collection_non_empty" name="@NAME@" folder="@FOLDER@" ext="@EXT@">
36 <expand macro="test_collection_element" id="NC_003450" 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_014008" 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_014363" 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_018014" 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_019904" folder="@FOLDER@" ext="@EXT@"/>
45 </expand>
46 </xml>
47
48 </macros>
49 <!-- TODO <xrefs>
50 <xref type="bio.tools"></xref>
51 </xrefs> -->
52 <requirements>
53 <requirement type="package" version="2.74.0">bioconductor-biostrings</requirement>
54 <requirement type="package" version="1.58.0">bioconductor-genomicranges</requirement>
55 <requirement type="package" version="1.18.0">bioconductor-gmoviz</requirement>
56 <requirement type="package" version="0.2.1">r-formattable</requirement>
57 <requirement type="package" version="1.0.1">r-here</requirement>
58 <requirement type="package" version="2.2.1">r-janitor</requirement>
59 <requirement type="package" version="1.4.0">r-kableextra</requirement>
60 <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="2.0.2">r-base64</requirement>
63 <requirement type="package" version="3.5.0">r-pdftools</requirement>
64 </requirements>
65 <command detect_errors="exit_code"><![CDATA[
66 mkdir -p data/genomes &&
67 #for e in $genomes
68 ln -s '$e' 'data/genomes/${e.element_identifier}.fna' &&
69 #end for
70
71 mkdir -p data/host_analyses &&
72 mkdir -p data/virus_analyses &&
73
74 ## checkm
75 mkdir -p data/host_analyses/checkm2 &&
76 ln -s '$checkm' data/host_analyses/checkm2/quality_report.tsv &&
77
78 ## defense-finder inputs
79 mkdir -p data/host_analyses/defense-finder &&
80 #for e in $defense_finder
81 mkdir -p 'data/host_analyses/defense-finder/${e.element_identifier}/' &&
82 ln -s '$e' 'data/host_analyses/defense-finder/${e.element_identifier}/${e.element_identifier}_defense_finder_systems.tsv' &&
83 #end for
84
85 ## genomad inputs
86 mkdir -p data/host_analyses/genomad &&
87 #for e in $genomad
88 mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' &&
89 ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus_summary.tsv' &&
90 #end for
91 #for e in $genomad_phages
92 mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' &&
93 ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus.fna' &&
94 #end for
95 #for e in $genomad_annotations
96 mkdir -p 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/' &&
97 ln -s '$e' 'data/host_analyses/genomad/${e.element_identifier}/${e.element_identifier}_summary/${e.element_identifier}_virus_genes.tsv' &&
98 #end for
99
100 ## GTDBTK
101 mkdir -p data/host_analyses/gtdbtk &&
102 ln -s '$gtdb_summary' data/host_analyses/gtdbtk/gtdbtk.bac120.summary.tsv &&
103
104 ## CheckV
105 mkdir -p data/virus_analyses/checkv &&
106 #for e in $checkv
107 mkdir -p 'data/virus_analyses/checkv/${e.element_identifier}/' &&
108 ln -s '$e' 'data/virus_analyses/checkv/${e.element_identifier}/quality_summary.tsv' &&
109 #end for
110
111 ## drep compare
112 mkdir -p data/virus_analyses/drep_compare &&
113 #for e in $drep_compare
114 mkdir -p 'data/virus_analyses/drep_compare/${e.element_identifier}/data_tables' &&
115 ln -s '$e' 'data/virus_analyses/drep_compare/${e.element_identifier}/data_tables/Cdb.csv' &&
116 #end for
117 #for e in $drep_compare_clustering_dendrogram
118 mkdir 'data/virus_analyses/drep_compare/${e.element_identifier}/figures/' &&
119 ln -s '$e' 'data/virus_analyses/drep_compare/${e.element_identifier}/figures/Primary_clustering_dendrogram.pdf' &&
120 #end for
121
122 ## iphop
123 mkdir -p data/virus_analyses/iphop &&
124 #for e in $iphop
125 mkdir -p 'data/virus_analyses/iphop/${e.element_identifier}/' &&
126 ln -s '$e' 'data/virus_analyses/iphop/${e.element_identifier}/Host_prediction_to_genome_m90.csv' &&
127 #end for
128
129 ## abricate
130 mkdir -p data/virus_analyses/abricate &&
131 #for e in $abricate
132 mkdir -p 'data/virus_analyses/abricate/${e.element_identifier}/' &&
133 ln -s '$e' 'data/virus_analyses/abricate/${e.element_identifier}/${e.element_identifier}_virus_vfdb.tsv' &&
134 #end for
135
136 ## vibrant
137 mkdir -p data/virus_analyses/vibrant &&
138 #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/' &&
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_${e.element_identifier}_virus.tsv' &&
141 #end for
142
143 Rscript -e "library(rmarkdown); render('$__tool_directory__/report.Rmd', output_dir='"\$(pwd)"', output_format = 'html_document', intermediates_dir = '"\$(pwd)"', knit_root_dir='"\$(pwd)"')" &&
144 cp report.html '$report'
145 ]]></command>
146 <inputs>
147 <param type="data_collection" name="genomes" format="fasta" label="Genomes"/>
148 <param type="data" name="checkm" format="tabular" label="Checkm2 quality report"/>
149 <param type="data_collection" name="genomad" format="tabular" label="geNomad Virus Summary"/>
150 <param type="data_collection" name="genomad_phages" format="fasta" label="geNomad Virus fasta"/>
151 <param type="data_collection" name="genomad_annotations" format="tabular" label="geNomad Virus genes"/>
152 <param type="data_collection" name="defense_finder" format="tabular" label="DefenseFinder systems"/>
153 <param type="data" name="gtdb_summary" format="tsv" label="GTDB-Tk summary"/>
154 <param type="data_collection" name="checkv" format="tabular" label="CheckV Quality summary"/>
155 <param type="data_collection" name="drep_compare" format="csv" label="drep compare Cdb.csv"/>
156 <param type="data_collection" name="drep_compare_clustering_dendrogram" format="pdf" label="drep compare clustering dendrogram"/>
157 <param type="data_collection" name="iphop" format="csv" label="iPHop Host prediction to genome"/>
158 <param type="data_collection" name="abricate" format="tabular" label="Abricate results"/>
159 <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'"/>
160 </inputs>
161 <outputs>
162 <data name="report" format="html"/>
163 </outputs>
164 <tests>
165 <test>
166 <!-- <expand macro="test_collection" name="genomes" folder="genomes" ext="fasta"/> -->
167 <param name="genomes">
168 <collection type="list">
169 <expand macro="zenodo_collection_element" id="NC_000913"/>
170 <expand macro="zenodo_collection_element" id="NC_002737"/>
171 <expand macro="zenodo_collection_element" id="NC_008261"/>
172 <expand macro="zenodo_collection_element" id="NC_009012"/>
173 <expand macro="zenodo_collection_element" id="NC_014168"/>
174 <expand macro="zenodo_collection_element" id="NC_014212"/>
175 <expand macro="zenodo_collection_element" id="NC_014364"/>
176 <expand macro="zenodo_collection_element" id="NC_015761"/>
177 <expand macro="zenodo_collection_element" id="NC_017033"/>
178 <expand macro="zenodo_collection_element" id="NC_018068"/>
179 <expand macro="zenodo_collection_element" id="NC_018515"/>
180 <expand macro="zenodo_collection_element" id="NC_019936"/>
181 <expand macro="zenodo_collection_element" id="NC_021184"/>
182 <expand macro="zenodo_collection_element" id="NC_003450"/>
183 <expand macro="zenodo_collection_element" id="NC_012982"/>
184 <expand macro="zenodo_collection_element" id="NC_014008"/>
185 <expand macro="zenodo_collection_element" id="NC_014211"/>
186 <expand macro="zenodo_collection_element" id="NC_014363"/>
187 <expand macro="zenodo_collection_element" id="NC_017095"/>
188 <expand macro="zenodo_collection_element" id="NC_018014"/>
189 <expand macro="zenodo_collection_element" id="NC_019897"/>
190 <expand macro="zenodo_collection_element" id="NC_019904"/>
191 </collection>
192 </param>
193 <param name="checkm" value="checkm2.Quality_report.tabular"/>
194 <expand macro="test_collection" name="genomad" folder="genomad_virus_summary" ext="tabular"/>
195 <expand macro="test_collection" name="genomad_phages" folder="genomad_virus_fasta" ext="fasta"/>
196 <expand macro="test_collection" name="genomad_annotations" folder="genomad_virus_genes" ext="tabular"/>
197 <expand macro="test_collection" name="defense_finder" folder="defense_finder_systems" ext="tabular"/>
198 <param name="gtdb_summary" value="gtdbtk.bac120.summary"/>
199 <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"/>
201 <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"/>
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"/>
205 <expand macro="test_collection_non_empty" name="vibrant" folder="vibrant_amg_individuals" ext="tabular"/>
206 <output name="report">
207 <assert_contents>
208 <has_size min="100"/>
209 <has_line line="&lt;html&gt;"/>
210 </assert_contents>
211 </output>
212 </test>
213 </tests>
214 <help><![CDATA[
215
216 .. class:: infomark
217
218 **What it does**
219
220 Create a report for the PHI toolkit workflow.
221
222 Usage
223 .....
224
225 **Input**
226
227 - Genomes
228 - Checkm2 quality report
229 - geNomad Virus Summary
230 - geNomad Virus genes
231 - DefenseFinder systems
232 - GTDB-Tk summary
233 - CheckV Quality summary
234 - drep compare Cdb.csv
235 - drep compare clustering dendrogram
236 - iPHop Host prediction to genome
237 - Abricate results
238 - Vibrant Individual predicted virus AMGs
239
240 **Output**
241
242 A html report summarizing the results.
243 ]]></help>
244 <!-- <citations>
245 <citation type="doi"> </citation>
246 </citations> -->
247 </tool>