Mercurial > repos > iuc > tooldistillator
comparison tooldistillator.xml @ 0:6e868bf6c38e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
author | iuc |
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date | Tue, 30 Apr 2024 08:42:33 +0000 |
parents | |
children | 65a69de1e294 |
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-1:000000000000 | 0:6e868bf6c38e |
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1 <tool id="tooldistillator" name="ToolDistillator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description> | |
3 Extract information from output files of specific tools and expose it as JSON files | |
4 </description> | |
5 <macros> | |
6 <import>macro.xml</import> | |
7 </macros> | |
8 <expand macro="biotools"/> | |
9 <expand macro="requirements"/> | |
10 <expand macro="version_command"/> | |
11 <command detect_errors="aggressive"><![CDATA[ | |
12 #import re | |
13 mkdir "tooldistillator_folder" && | |
14 | |
15 #set $counter = len($tool_section.tools)-1 | |
16 #for $i, $tool in enumerate( $tool_section.tools ) | |
17 tooldistillator | |
18 $tool.select_tool.tool_list | |
19 --hid '$tool.select_tool.input.hid' | |
20 '$tool.select_tool.input' | |
21 --analysis_software_version '$tool.select_tool.analysis_software_version' | |
22 --reference_database_version '$tool.select_tool.reference_database_version' | |
23 #if $tool.select_tool.tool_list == 'bakta' | |
24 #if $tool.select_tool.annotation_tabular_path | |
25 --annotation_tabular_path '$tool.select_tool.annotation_tabular_path' | |
26 --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid' | |
27 #end if | |
28 #if $tool.select_tool.annotation_genbank_path | |
29 --annotation_genbank_path '$tool.select_tool.annotation_genbank_path' | |
30 --annotation_genbank_hid '$tool.select_tool.annotation_genbank_path.hid' | |
31 #end if | |
32 #if $tool.select_tool.annotation_embl_path | |
33 --annotation_embl_path '$tool.select_tool.annotation_embl_path' | |
34 --annotation_embl_hid '$tool.select_tool.annotation_embl_path.hid' | |
35 #end if | |
36 #if $tool.select_tool.contig_sequences_path | |
37 --contig_sequences_path '$tool.select_tool.contig_sequences_path' | |
38 --contig_sequences_hid '$tool.select_tool.contig_sequences_path.hid' | |
39 #end if | |
40 #if $tool.select_tool.nucleotide_annotation_path | |
41 --nucleotide_annotation_path '$tool.select_tool.nucleotide_annotation_path' | |
42 --nucleotide_annotation_hid '$tool.select_tool.nucleotide_annotation_path.hid' | |
43 #end if | |
44 #if $tool.select_tool.amino_acid_annotation_path | |
45 --amino_acid_annotation_path '$tool.select_tool.amino_acid_annotation_path' | |
46 --amino_acid_annotation_hid '$tool.select_tool.amino_acid_annotation_path.hid' | |
47 #end if | |
48 #if $tool.select_tool.summary_result_path | |
49 --summary_result_path '$tool.select_tool.summary_result_path' | |
50 --summary_result_hid '$tool.select_tool.summary_result_path.hid' | |
51 #end if | |
52 #if $tool.select_tool.gff_file_path | |
53 --gff_file_path '$tool.select_tool.gff_file_path' | |
54 --gff_file_hid '$tool.select_tool.gff_file_path.hid' | |
55 #end if | |
56 #if $tool.select_tool.hypothetical_protein_path | |
57 --hypothetical_protein_path '$tool.select_tool.hypothetical_protein_path' | |
58 --hypothetical_protein_hid '$tool.select_tool.hypothetical_protein_path.hid' | |
59 #end if | |
60 #if $tool.select_tool.hypothetical_tabular_path | |
61 --hypothetical_tabular_path '$tool.select_tool.hypothetical_tabular_path' | |
62 --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid' | |
63 #end if | |
64 #if $tool.select_tool.plot_file_path | |
65 --plot_file_path '$tool.select_tool.plot_file_path' | |
66 --plot_file_hid '$tool.select_tool.plot_file_path.hid' | |
67 #end if | |
68 #elif $tool.select_tool.tool_list == 'bandage': | |
69 #if $tool.select_tool.bandage_plot_path | |
70 --bandage_plot_path '$tool.select_tool.bandage_plot_path' | |
71 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid' | |
72 #end if | |
73 #elif $tool.select_tool.tool_list == 'bracken': | |
74 #if $tool.select_tool.kraken_report_path | |
75 --kraken_report_path '$tool.select_tool.kraken_report_path' | |
76 --kraken_report_hid '$tool.select_tool.kraken_report_path.hid' | |
77 #end if | |
78 --threshold '$tool.select_tool.threshold' | |
79 --read_len '$tool.select_tool.read_len' | |
80 --level '$tool.select_tool.level' | |
81 #elif $tool.select_tool.tool_list == 'fastp': | |
82 #if $tool.select_tool.trimmed_forward_R1_path | |
83 --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path' | |
84 --trimmed_forward_R1_hid '$tool.select_tool.trimmed_forward_R1_path.hid' | |
85 #end if | |
86 #if $tool.select_tool.trimmed_reverse_R2_path | |
87 --trimmed_reverse_R2_path '$tool.select_tool.trimmed_reverse_R2_path' | |
88 --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid' | |
89 #end if | |
90 #if $tool.select_tool.html_report_path | |
91 --html_report_path '$tool.select_tool.html_report_path' | |
92 --html_report_hid '$tool.select_tool.html_report_path.hid' | |
93 #end if | |
94 #elif $tool.select_tool.tool_list == 'integronfinder2': | |
95 #if $tool.select_tool.summary_file_path | |
96 --summary_file_path '$tool.select_tool.summary_file_path' | |
97 --summary_file_hid '$tool.select_tool.summary_file_path.hid' | |
98 #end if | |
99 #elif $tool.select_tool.tool_list == 'isescan': | |
100 #if $tool.select_tool.summary_path | |
101 --summary_path '$tool.select_tool.summary_path' | |
102 --summary_hid '$tool.select_tool.summary_path.hid' | |
103 #end if | |
104 #if $tool.select_tool.annotation_path | |
105 --annotation_path '$tool.select_tool.annotation_path' | |
106 --annotation_hid '$tool.select_tool.annotation_path.hid' | |
107 #end if | |
108 #if $tool.select_tool.orf_fna_path | |
109 --orf_fna_path '$tool.select_tool.orf_fna_path' | |
110 --orf_fna_hid '$tool.select_tool.orf_fna_path.hid' | |
111 #end if | |
112 #if $tool.select_tool.orf_faa_path | |
113 --orf_faa_path '$tool.select_tool.orf_faa_path' | |
114 --orf_faa_hid '$tool.select_tool.orf_faa_path.hid' | |
115 #end if | |
116 #if $tool.select_tool.is_fna_path | |
117 --is_fna_path '$tool.select_tool.is_fna_path' | |
118 --is_fna_hid '$tool.select_tool.is_fna_path.hid' | |
119 #end if | |
120 #elif $tool.select_tool.tool_list == 'kraken2': | |
121 #if $tool.select_tool.seq_classification_file_path | |
122 --seq_classification_file_path '$tool.select_tool.seq_classification_file_path' | |
123 --seq_classification_file_hid '$tool.select_tool.seq_classification_file_path.hid' | |
124 #end if | |
125 #elif $tool.select_tool.tool_list == 'plasmidfinder': | |
126 #if $tool.select_tool.plasmid_result_tabular_path | |
127 --plasmid_result_tabular_path '$tool.select_tool.plasmid_result_tabular_path' | |
128 --plasmid_result_tabular_hid '$tool.select_tool.plasmid_result_tabular_path.hid' | |
129 #end if | |
130 #if $tool.select_tool.genome_hit_path | |
131 --genome_hit_path '$tool.select_tool.genome_hit_path' | |
132 --genome_hit_hid '$tool.select_tool.genome_hit_path.hid' | |
133 #end if | |
134 #if $tool.select_tool.plasmid_hit_path | |
135 --plasmid_hit_path '$tool.select_tool.plasmid_hit_path' | |
136 --plasmid_hit_hid '$tool.select_tool.plasmid_hit_path.hid' | |
137 #end if | |
138 #elif $tool.select_tool.tool_list == 'quast': | |
139 #if $tool.select_tool.quast_html_path | |
140 --quast_html_path '$tool.select_tool.quast_html_path' | |
141 --quast_html_hid '$tool.select_tool.quast_html_path.hid' | |
142 #end if | |
143 #elif $tool.select_tool.tool_list == 'recentrifuge': | |
144 #if $tool.select_tool.rcf_stat_path | |
145 --rcf_stat_path '$tool.select_tool.rcf_stat_path' | |
146 --rcf_stat_hid '$tool.select_tool.rcf_stat_path.hid' | |
147 #end if | |
148 #if $tool.select_tool.rcf_html_path | |
149 --rcf_html_path '$tool.select_tool.rcf_html_path' | |
150 --rcf_html_hid '$tool.select_tool.rcf_html_path.hid' | |
151 #end if | |
152 #elif $tool.select_tool.tool_list == 'shovill': | |
153 #if $tool.select_tool.contig_graph_path | |
154 --contig_graph_path '$tool.select_tool.contig_graph_path' | |
155 --contig_graph_hid '$tool.select_tool.contig_graph_path.hid' | |
156 #end if | |
157 #if $tool.select_tool.bam_file_path | |
158 --bam_file_path '$tool.select_tool.bam_file_path' | |
159 --bam_file_hid '$tool.select_tool.bam_file_path.hid' | |
160 #end if | |
161 #elif $tool.select_tool.tool_list == 'staramr': | |
162 #if $tool.select_tool.mlst_file_path | |
163 --mlst_file_path '$tool.select_tool.mlst_file_path' | |
164 --mlst_file_hid '$tool.select_tool.mlst_file_path.hid' | |
165 #end if | |
166 #if $tool.select_tool.plasmidfinder_file_path | |
167 --plasmidfinder_file_path '$tool.select_tool.plasmidfinder_file_path' | |
168 --plasmidfinder_file_hid '$tool.select_tool.plasmidfinder_file_path.hid' | |
169 #end if | |
170 #if $tool.select_tool.pointfinder_file_path | |
171 --pointfinder_file_path '$tool.select_tool.pointfinder_file_path' | |
172 --pointfinder_file_hid '$tool.select_tool.pointfinder_file_path.hid' | |
173 #end if | |
174 #if $tool.select_tool.setting_file_path | |
175 --setting_file_path '$tool.select_tool.setting_file_path' | |
176 --setting_file_hid '$tool.select_tool.setting_file_path.hid' | |
177 #end if | |
178 #elif $tool.select_tool.tool_list == 'tabular_file': | |
179 --analysis_software_name '$tool.select_tool.analysis_software_name' | |
180 #end if | |
181 -o 'tooldistillator_folder/$($tool.select_tool.tool_list)_$(i)_output.json' | |
182 | tee '$logfile' | |
183 #if $i < $counter | |
184 && | |
185 #end if | |
186 #end for | |
187 ]]> | |
188 </command> | |
189 <inputs> | |
190 <section name="tool_section" title="Available tools" expanded="true"> | |
191 <repeat name="tools" title="Tool" min="0"> | |
192 <conditional name="select_tool"> | |
193 <param name="tool_list" type="select" label="Available tools"> | |
194 <option value="abricate">abricate</option> | |
195 <option value="bakta">bakta</option> | |
196 <option value="bandage">bandage</option> | |
197 <option value="bracken">bracken</option> | |
198 <option value="fastp">fastp</option> | |
199 <option value="integronfinder2">integronfinder2</option> | |
200 <option value="isescan">isescan</option> | |
201 <option value="kraken2">kraken2</option> | |
202 <option value="multiqc">MultiQC</option> | |
203 <option value="plasmidfinder">plasmidfinder</option> | |
204 <option value="quast">quast</option> | |
205 <option value="recentrifuge">recentrifuge</option> | |
206 <option value="refseqmasher">refseqmasher</option> | |
207 <option value="shovill">shovill</option> | |
208 <option value="staramr">staramr</option> | |
209 <option value="tabular_file">tabular_generic_file</option> | |
210 </param> | |
211 <when value="abricate"> | |
212 <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/> | |
213 <expand macro="analysis_software_version"/> | |
214 <expand macro="reference_database_version"/> | |
215 </when> | |
216 <when value="bakta"> | |
217 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/> | |
218 <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/> | |
219 <param argument="--annotation_genbank_path" type="data" format="txt" multiple="false" optional="true" label="Bakta genbank file" help="Genbank annotation file"/> | |
220 <param argument="--annotation_embl_path" type="data" format="txt" multiple="false" optional="true" label="Bakta embl file" help="EMBL annotation file"/> | |
221 <param argument="--contig_sequences_path" type="data" format="fasta" multiple="false" optional="true" label="Contig sequences" help="Contig sequences files"/> | |
222 <param argument="--hypothetical_protein_path" type="data" format="fasta" multiple="false" optional="true" label="Hypothetical protein" help="Hypothetical protein fasta file"/> | |
223 <param argument="--hypothetical_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Hypothetical annotation" help="Hypothetical protein annotation"/> | |
224 <param argument="--plot_file_path" type="data" format="svg" multiple="false" optional="true" label="Plot file" help="Plot of the annotation in svg format"/> | |
225 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/> | |
226 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide annotation" help="Nucleotide sequence annotation file"/> | |
227 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta protein annotation" help="Amino acid sequence annotation file"/> | |
228 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file in gff"/> | |
229 <expand macro="analysis_software_version"/> | |
230 <expand macro="reference_database_version"/> | |
231 </when> | |
232 <when value="bandage"> | |
233 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/> | |
234 <param argument="--bandage_plot_path" type="data" format="svg" multiple="false" optional="true" label="Bandage plot" help="Bandage visualisation file"/> | |
235 <expand macro="analysis_software_version"/> | |
236 <expand macro="reference_database_version"/> | |
237 </when> | |
238 <when value="bracken"> | |
239 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/> | |
240 <expand macro="analysis_software_version"/> | |
241 <expand macro="reference_database_version"/> | |
242 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Kraken re-estimated report" help="New kraken report from bracken tool"/> | |
243 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/> | |
244 <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/> | |
245 <param argument="--level" type="select" label="Taxonomic level estimation" optional="true" help="Level of final abundance (from Domain to subspecies, default on species)"> | |
246 <option value="D">Domain</option> | |
247 <option value="P">Phylum</option> | |
248 <option value="C">Class</option> | |
249 <option value="O">Order</option> | |
250 <option value="F">Family</option> | |
251 <option value="G">Genus</option> | |
252 <option value="S">Species</option> | |
253 <option value="S+">Subspecies</option> | |
254 </param> | |
255 </when> | |
256 <when value="fastp"> | |
257 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/> | |
258 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/> | |
259 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/> | |
260 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/> | |
261 <expand macro="analysis_software_version"/> | |
262 <expand macro="reference_database_version"/> | |
263 </when> | |
264 <when value="integronfinder2"> | |
265 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/> | |
266 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Summary report" help="Summary file from integronfinder2"/> | |
267 <expand macro="analysis_software_version"/> | |
268 <expand macro="reference_database_version"/> | |
269 </when> | |
270 <when value="isescan"> | |
271 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/> | |
272 <param argument="--summary_path" type="data" format="tabular" optional="true" multiple="false" label="summary file" help="ISEscan summary"/> | |
273 <param argument="--annotation_path" type="data" format="gff" optional="true" multiple="false" label="annotation results" help="Annotation in gff file format"/> | |
274 <param argument="--orf_fna_path" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/> | |
275 <param argument="--orf_faa_path" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/> | |
276 <param argument="--is_fna_path" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/> | |
277 <expand macro="analysis_software_version"/> | |
278 <expand macro="reference_database_version"/> | |
279 </when> | |
280 <when value="kraken2"> | |
281 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/> | |
282 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/> | |
283 <expand macro="analysis_software_version"/> | |
284 <expand macro="reference_database_version"/> | |
285 </when> | |
286 <when value="multiqc"> | |
287 <param name="input" type="data" format="html" multiple="false" label="MultiQC report" help="Html report from MultiQC"/> | |
288 <expand macro="analysis_software_version"/> | |
289 <expand macro="reference_database_version"/> | |
290 </when> | |
291 <when value="plasmidfinder"> | |
292 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> | |
293 <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/> | |
294 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> | |
295 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> | |
296 <expand macro="analysis_software_version"/> | |
297 <expand macro="reference_database_version"/> | |
298 </when> | |
299 <when value="quast"> | |
300 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/> | |
301 <param argument="--quast_html_path" type="data" format="html" multiple="false" optional="true" label="Quast html report" help="Quast html report"/> | |
302 <expand macro="analysis_software_version"/> | |
303 <expand macro="reference_database_version"/> | |
304 </when> | |
305 <when value="recentrifuge"> | |
306 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/> | |
307 <param argument="--rcf_stat_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/> | |
308 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/> | |
309 <expand macro="analysis_software_version"/> | |
310 <expand macro="reference_database_version"/> | |
311 </when> | |
312 <when value="refseqmasher"> | |
313 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/> | |
314 <expand macro="analysis_software_version"/> | |
315 <expand macro="reference_database_version"/> | |
316 </when> | |
317 <when value="shovill"> | |
318 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/> | |
319 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/> | |
320 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/> | |
321 <expand macro="analysis_software_version"/> | |
322 <expand macro="reference_database_version"/> | |
323 </when> | |
324 <when value="staramr"> | |
325 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/> | |
326 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/> | |
327 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/> | |
328 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/> | |
329 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/> | |
330 <expand macro="analysis_software_version"/> | |
331 <expand macro="reference_database_version"/> | |
332 </when> | |
333 <when value="tabular_file"> | |
334 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/> | |
335 <param argument="--analysis_software_name" type="text" multiple="false" optional="true" label="Tool name" help="Tool name which generated the result file"/> | |
336 <expand macro="analysis_software_version"/> | |
337 <expand macro="reference_database_version"/> | |
338 </when> | |
339 </conditional> | |
340 </repeat> | |
341 </section> | |
342 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/> | |
343 </inputs> | |
344 <outputs> | |
345 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: JSON"> | |
346 <discover_datasets pattern="(?P<designation>.+)\.json" format="json" directory="tooldistillator_folder" /> | |
347 </collection> | |
348 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log"> | |
349 <filter> log == True </filter> | |
350 </data> | |
351 </outputs> | |
352 <tests> | |
353 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile --> | |
354 <section name="tool_section"> | |
355 <repeat name="tools"> | |
356 <conditional name="select_tool"> | |
357 <param name="tool_list" value="abricate"/> | |
358 <param name="input" value="abricate/report.tsv" ftype="tabular"/> | |
359 <param name="analysis_software_version" value="1.0"/> | |
360 <param name="reference_database_version" value="2.0" /> | |
361 </conditional> | |
362 </repeat> | |
363 </section> | |
364 <param name="log" value="true"/> | |
365 <output_collection name="output_json" type="list"> | |
366 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> | |
367 </output_collection> | |
368 <output name="logfile" compare="sim_size" > | |
369 <assert_contents><has_size value="0"/></assert_contents> | |
370 </output> | |
371 </test> | |
372 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files --> | |
373 <section name="tool_section"> | |
374 <repeat name="tools"> | |
375 <conditional name="select_tool"> | |
376 <param name="tool_list" value="bakta"/> | |
377 <param name="input" value="bakta/bakta.json" ftype="json"/> | |
378 <param name="annotation_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
379 <param name="annotation_genbank_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
380 <param name="annotation_embl_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
381 <param name="contig_sequences_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
382 <param name="hypothetical_protein_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
383 <param name="hypothetical_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
384 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
385 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/> | |
386 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/> | |
387 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/> | |
388 <param name="analysis_software_version" value="1.8.1"/> | |
389 <param name="reference_database_version" value="5.0"/> | |
390 </conditional> | |
391 </repeat> | |
392 </section> | |
393 <output_collection name="output_json" type="list" count="1"> | |
394 <expand macro="element_assert" name="bakta_0_output" text="hypothetical protein"/> | |
395 </output_collection> | |
396 </test> | |
397 <test expect_num_outputs="1"> <!-- TEST_3 bakta with no files --> | |
398 <section name="tool_section"> | |
399 <repeat name="tools"> | |
400 <conditional name="select_tool"> | |
401 <param name="tool_list" value="bakta"/> | |
402 <param name="input" value="bakta/bakta.json" ftype="json"/> | |
403 </conditional> | |
404 </repeat> | |
405 </section> | |
406 <output_collection name="output_json" type="list" count="1"> | |
407 <expand macro="element_assert" name="bakta_0_output" text="hypothetical protein"/> | |
408 </output_collection> | |
409 </test> | |
410 <test expect_num_outputs="1"> <!-- TEST_4 All tool in repeat --> | |
411 <section name="tool_section"> | |
412 <repeat name="tools"> | |
413 <conditional name="select_tool"> | |
414 <param name="tool_list" value="abricate"/> | |
415 <param name="input" value="abricate/report.tsv" ftype="tabular"/> | |
416 <param name="analysis_software_version" value="1.0"/> | |
417 <param name="reference_database_version" value="2.0" /> | |
418 </conditional> | |
419 </repeat> | |
420 <repeat name="tools"> | |
421 <conditional name="select_tool"> | |
422 <param name="tool_list" value="bakta"/> | |
423 <param name="input" value="bakta/bakta.json" ftype="json"/> | |
424 <param name="annotation_tabular_path" value="bakta/bakta_annotation.tsv" ftype="tabular"/> | |
425 <param name="annotation_genbank_path" value="bakta/bakta_gbff.gbff"/> | |
426 <param name="annotation_embl_path" value="bakta/bakta_embl.embl"/> | |
427 <param name="contig_sequences_path" value="bakta/bakta_contigs_sequences.fna" ftype="fasta"/> | |
428 <param name="hypothetical_protein_path" value="bakta/bakta_hypothetical.faa" ftype="fasta"/> | |
429 <param name="hypothetical_tabular_path" value="bakta/bakta_hypothetical.tsv" ftype="tabular"/> | |
430 <param name="plot_file_path" value="bakta/bakta_plot.svg"/> | |
431 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/> | |
432 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/> | |
433 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/> | |
434 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/> | |
435 <param name="analysis_software_version" value="1.8.1"/> | |
436 <param name="reference_database_version" value="5.0"/> | |
437 </conditional> | |
438 </repeat> | |
439 <repeat name="tools"> | |
440 <conditional name="select_tool"> | |
441 <param name="tool_list" value="bandage"/> | |
442 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/> | |
443 <param name="bandage_plot_path" value="bandage/bandage_plot.svg"/> | |
444 <param name="analysis_software_version" value="1.0"/> | |
445 <param name="reference_database_version" value="1.0"/> | |
446 </conditional> | |
447 </repeat> | |
448 <repeat name="tools"> | |
449 <conditional name="select_tool"> | |
450 <param name="tool_list" value="bracken"/> | |
451 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/> | |
452 <param name="kraken_report_path" value="bracken/bracken_kraken_report.tsv"/> | |
453 <param name="read_len" value="100"/> | |
454 <param name="level" value="S"/> | |
455 <param name="threshold" value="1"/> | |
456 <param name="analysis_software_version" value="1.0"/> | |
457 <param name="reference_database_version" value="1.0"/> | |
458 </conditional> | |
459 </repeat> | |
460 <repeat name="tools"> | |
461 <conditional name="select_tool"> | |
462 <param name="tool_list" value="fastp"/> | |
463 <param name="input" value="fastp/fastp_report.json" ftype="json"/> | |
464 <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/> | |
465 <param name="trimmed_reverse_R2_path" value="fastp/trimmed_R2.fastq.gz"/> | |
466 <param name="html_report_path" value="fastp/fastp_report.html"/> | |
467 <param name="analysis_software_version" value="1.0"/> | |
468 <param name="reference_database_version" value="1.0"/> | |
469 </conditional> | |
470 </repeat> | |
471 <repeat name="tools"> | |
472 <conditional name="select_tool"> | |
473 <param name="tool_list" value="integronfinder2"/> | |
474 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/> | |
475 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/> | |
476 <param name="analysis_software_version" value="1.0"/> | |
477 <param name="reference_database_version" value="1.0"/> | |
478 </conditional> | |
479 </repeat> | |
480 <repeat name="tools"> | |
481 <conditional name="select_tool"> | |
482 <param name="tool_list" value="isescan"/> | |
483 <param name="input" value="isescan/results.tsv" ftype="tabular"/> | |
484 <param name="summary_path" value="isescan/summary.tsv"/> | |
485 <param name="annotation_path" value="isescan/annotation.gff"/> | |
486 <param name="orf_fna_path" value="isescan/orf.fna"/> | |
487 <param name="orf_faa_path" value="isescan/orf.faa"/> | |
488 <param name="is_fna_path" value="isescan/is.fna"/> | |
489 <param name="analysis_software_version" value="1.0"/> | |
490 <param name="reference_database_version" value="1.0"/> | |
491 </conditional> | |
492 </repeat> | |
493 <repeat name="tools"> | |
494 <conditional name="select_tool"> | |
495 <param name="tool_list" value="kraken2"/> | |
496 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/> | |
497 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/> | |
498 <param name="analysis_software_version" value="1.0"/> | |
499 <param name="reference_database_version" value="1.0"/> | |
500 </conditional> | |
501 </repeat> | |
502 <repeat name="tools"> | |
503 <conditional name="select_tool"> | |
504 <param name="tool_list" value="plasmidfinder"/> | |
505 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/> | |
506 <param name="genome_hit_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/> | |
507 <param name="plasmid_hit_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/> | |
508 <param name="analysis_software_version" value="1.0"/> | |
509 <param name="reference_database_version" value="1.0"/> | |
510 </conditional> | |
511 </repeat> | |
512 <repeat name="tools"> | |
513 <conditional name="select_tool"> | |
514 <param name="tool_list" value="quast"/> | |
515 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/> | |
516 <param name="quast_html_path" value="quast/quast_report.html"/> | |
517 <param name="analysis_software_version" value="1.0"/> | |
518 <param name="reference_database_version" value="1.0"/> | |
519 </conditional> | |
520 </repeat> | |
521 <repeat name="tools"> | |
522 <conditional name="select_tool"> | |
523 <param name="tool_list" value="recentrifuge"/> | |
524 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/> | |
525 <param name="rcf_stat_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/> | |
526 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/> | |
527 <param name="analysis_software_version" value="1.0"/> | |
528 <param name="reference_database_version" value="1.0"/> | |
529 </conditional> | |
530 </repeat> | |
531 <repeat name="tools"> | |
532 <conditional name="select_tool"> | |
533 <param name="tool_list" value="refseqmasher"/> | |
534 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/> | |
535 <param name="analysis_software_version" value="1.0"/> | |
536 <param name="reference_database_version" value="1.0"/> | |
537 </conditional> | |
538 </repeat> | |
539 <repeat name="tools"> | |
540 <conditional name="select_tool"> | |
541 <param name="tool_list" value="shovill"/> | |
542 <param name="input" value="shovill/contigs.fa" ftype="fasta"/> | |
543 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/> | |
544 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/> | |
545 <param name="analysis_software_version" value="1.0"/> | |
546 <param name="reference_database_version" value="1.0"/> | |
547 </conditional> | |
548 </repeat> | |
549 <repeat name="tools"> | |
550 <conditional name="select_tool"> | |
551 <param name="tool_list" value="staramr"/> | |
552 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/> | |
553 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/> | |
554 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/> | |
555 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/> | |
556 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/> | |
557 <param name="analysis_software_version" value="1.0"/> | |
558 <param name="reference_database_version" value="1.0"/> | |
559 </conditional> | |
560 </repeat> | |
561 <repeat name="tools"> | |
562 <conditional name="select_tool"> | |
563 <param name="tool_list" value="tabular_file"/> | |
564 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/> | |
565 <param name="analysis_software_name" value="test_galaxy"/> | |
566 <param name="analysis_software_version" value="1.0"/> | |
567 <param name="reference_database_version" value="1.0"/> | |
568 </conditional> | |
569 </repeat> | |
570 </section> | |
571 <output_collection name="output_json" type="list" count="15"> | |
572 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> | |
573 <expand macro="element_assert" name="bakta_1_output" text="hypothetical protein"/> | |
574 <expand macro="element_assert" name="bandage_2_output" text="3042326"/> | |
575 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/> | |
576 <expand macro="element_assert" name="fastp_4_output" text="705053822"/> | |
577 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/> | |
578 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/> | |
579 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis"/> | |
580 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/> | |
581 <expand macro="element_assert" name="quast_9_output" text="2944723"/> | |
582 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/> | |
583 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/> | |
584 <expand macro="element_assert" name="shovill_12_output" text="436224"/> | |
585 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/> | |
586 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/> | |
587 </output_collection> | |
588 </test> | |
589 | |
590 </tests> | |
591 <help><![CDATA[ | |
592 **What it does** | |
593 | |
594 ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools. | |
595 | |
596 This tool here is extracting information from output files of specific tools and exposing it as JSON files | |
597 ** Tool input** | |
598 | |
599 ToolDistillator can use several input type from at least 14 different tools : | |
600 | |
601 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
602 | Tools | Version | Default input file| Optional files | | |
603 | Abricate | 1.0.1 | output.tsv | | | |
604 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
605 | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | | |
606 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
607 | Bandage | 0.8.1 | info.txt | | | |
608 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
609 | Bracken | 2.8 | output.tsv | taxonomy.tsv | | |
610 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
611 | Fastp | 0.23.2 | output.json | | | |
612 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
613 | Integronfinder2| 2.0.2 | output.integrons | output.summary | | |
614 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
615 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | | |
616 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
617 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | | |
618 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
619 | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | | |
620 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
621 | Quast | 5.2.0 | output.tsv | | | |
622 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
623 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | | |
624 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
625 | Refseqmasher | 0.1.2 | output.tsv | | | |
626 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
627 | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | | |
628 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
629 | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | | |
630 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
631 | tabular_file | 0 | output.tsv | no optional files | | |
632 +----------------+----------------+-------------------+------------------------------------------------------------+ | |
633 | |
634 ** Options ** | |
635 | |
636 You can add a tool version and a database version for related tools. | |
637 For some tools you can add optional files previously produced by the tool | |
638 | |
639 ]]></help> | |
640 <expand macro="citations"/> | |
641 </tool> |