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comparison bakta.xml @ 4:3f0aa1b3e816 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
author iuc
date Mon, 24 Jul 2023 11:22:16 +0000
parents 865ece5ca178
children 728dacaf08a9
comparison
equal deleted inserted replaced
3:865ece5ca178 4:3f0aa1b3e816
9 <expand macro='xrefs'/> 9 <expand macro='xrefs'/>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <expand macro="version_command"/> 11 <expand macro="version_command"/>
12 12
13 <command detect_errors="aggressive"><![CDATA[ 13 <command detect_errors="aggressive"><![CDATA[
14
14 mkdir -p ./database_path/amrfinderplus-db && 15 mkdir -p ./database_path/amrfinderplus-db &&
15 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path && 16 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path &&
16 ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest && 17 ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
17 bakta 18 bakta --verbose
19
18 #*====================================== 20 #*======================================
19 CPU option 21 CPU option
20 ======================================*# 22 ======================================*#
21 --threads \${GALAXY_SLOTS:-1} 23 --threads \${GALAXY_SLOTS:-1}
22 #*====================================== 24 #*======================================
23 Bakta database 25 Bakta database
24 ======================================*# 26 ======================================*#
25 --db ./database_path 27 --db './database_path'
28 --output 'bakta_output'
26 #if $input_option.min_contig_length 29 #if $input_option.min_contig_length
27 --min-contig-length $input_option.min_contig_length 30 --min-contig-length $input_option.min_contig_length
28 #else if $annotation.compliant 31 #else if $annotation.compliant
29 --min-contig-length 200 32 --min-contig-length 200
30 #else 33 #else
86 <inputs> 89 <inputs>
87 <!-- DB and file INPUT --> 90 <!-- DB and file INPUT -->
88 <section name="input_option" title="Input/Output options" expanded="true"> 91 <section name="input_option" title="Input/Output options" expanded="true">
89 <param name="bakta_db_select" type="select" label="The bakta database"> 92 <param name="bakta_db_select" type="select" label="The bakta database">
90 <options from_data_table="bakta_database"> 93 <options from_data_table="bakta_database">
91 <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/> 94 <filter type="static_value" value="@COMPATIBLE_BAKTA_VERSION@" column="bakta_version"/>
92 <validator message="No bakta database is available" type="no_options"/> 95 <validator message="No bakta database is available" type="no_options"/>
93 </options> 96 </options>
94 </param> 97 </param>
95 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> 98 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
96 <options from_data_table="amrfinderplus_database"> 99 <options from_data_table="amrfinderplus_database">
97 <validator message="No amrfinderplus database is available" type="no_options"/> 100 <validator message="No amrfinderplus database is available" type="no_options"/>
126 </param> 129 </param>
127 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/> 130 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>
128 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> 131 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
129 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/> 132 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
130 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/> 133 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
134 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/>
131 </section> 135 </section>
132 <!-- PARAMETER FOR WORKFLOW ANALYSIS --> 136 <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
133 <section name="workflow" title="Workflow option to skip steps"> 137 <section name="workflow" title="Workflow option to skip steps">
134 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip"> 138 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">
135 <option value="--skip-trna"> Skip tRNA detection and annotation </option> 139 <option value="--skip-trna">Skip tRNA detection and annotation</option>
136 <option value="--skip-tmrna"> Skip tmRNA detection and annotation </option> 140 <option value="--skip-tmrna">Skip tmRNA detection and annotation</option>
137 <option value="--skip-rrna"> Skip rRNA detection and annotation </option> 141 <option value="--skip-rrna">Skip rRNA detection and annotation</option>
138 <option value="--skip-ncrna"> Skip ncRNA detection and annotation </option> 142 <option value="--skip-ncrna">Skip ncRNA detection and annotation</option>
139 <option value="--skip-ncrna-region"> Skip ncRNA region detection and annotation </option> 143 <option value="--skip-ncrna-region">Skip ncRNA region detection and annotation</option>
140 <option value="--skip-crispr"> Skip CRISPR array detection and annotation </option> 144 <option value="--skip-crispr">Skip CRISPR array detection and annotation</option>
141 <option value="--skip-cds"> Skip CDS detection and annotation </option> 145 <option value="--skip-cds">Skip CDS detection and annotation</option>
142 <option value="--skip-pseudo"> Skip pseudogene detection and annotation </option> 146 <option value="--skip-pseudo">Skip pseudogene detection and annotation</option>
143 <option value="--skip-sorf"> Skip sORF detection and annotation </option> 147 <option value="--skip-sorf">Skip sORF detection and annotation</option>
144 <option value="--skip-gap"> Skip gap detection and annotation </option> 148 <option value="--skip-gap">Skip gap detection and annotation</option>
145 <option value="--skip-ori"> Skip oriC/oriT detection and annotation </option> 149 <option value="--skip-ori">Skip oriC/oriT detection and annotation</option>
150 <option value="--skip-plot">Skip generation of circular genome plots</option>
146 </param> 151 </param>
147 </section> 152 </section>
148 <section name="output_files" title="Selection of the output files"> 153 <section name="output_files" title="Selection of the output files">
149 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> 154 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
150 <option value="file_tsv" selected="true"> Annotation file in TSV </option> 155 <option value="file_tsv" selected="true">Annotation file in TSV</option>
151 <option value="file_gff3" selected="true"> Annotation and sequence in GFF3 </option> 156 <option value="file_gff3" selected="true">Annotation and sequence in GFF3</option>
152 <option value="file_gbff" selected="false"> Annotations and sequences in GenBank format </option> 157 <option value="file_gbff" selected="false">Annotations and sequences in GenBank format</option>
153 <option value="file_embl" selected="false"> Annotations and sequences in EMBL format </option> 158 <option value="file_embl" selected="false">Annotations and sequences in EMBL format</option>
154 <option value="file_fna" selected="false"> Replicon/contig DNA sequences as FASTA </option> 159 <option value="file_fna" selected="false">Replicon/contig DNA sequences as FASTA</option>
155 <option value="file_ffn" selected="true"> Feature nucleotide sequences as FASTA </option> 160 <option value="file_ffn" selected="true">Feature nucleotide sequences as FASTA</option>
156 <option value="file_faa" selected="false"> CDS/sORF amino acid sequences as FASTA </option> 161 <option value="file_faa" selected="false">CDS/sORF amino acid sequences as FASTA</option>
157 <option value="hypo_tsv" selected="false"> Hypothetical protein CDS in TSV</option> 162 <option value="hypo_tsv" selected="false">Hypothetical protein CDS in TSV</option>
158 <option value="hypo_fa" selected="false"> Hypothetical protein CDS amino sequences as FASTA</option> 163 <option value="hypo_fa" selected="false">Hypothetical protein CDS amino sequences as FASTA</option>
159 <option value="sum_txt" selected="false"> Summary as TXT</option> 164 <option value="sum_txt" selected="false">Summary as TXT</option>
160 <option value="file_json" selected="false"> Information on each annotated feature as JSON </option> 165 <option value="file_json" selected="false">Information on each annotated feature as JSON</option>
161 <option value="file_plot" selected="true"> Plot of the annotation result as SVG </option> 166 <option value="file_plot" selected="true">Plot of the annotation result as SVG</option>
162 <option value="log_txt" selected="false"> Log file as TXT </option> 167 <option value="log_txt" selected="false">Log file as TXT</option>
163 </param> 168 </param>
164 </section> 169 </section>
165 170
166 </inputs> 171 </inputs>
167 <outputs> 172 <outputs>
168 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary"> 173 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary">
169 <filter> output_files['output_selection'] and "file_tsv" in output_files['output_selection'] </filter> 174 <filter>output_files['output_selection'] and "file_tsv" in output_files['output_selection']</filter>
170 </data> 175 </data>
171 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences"> 176 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output/bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences">
172 <filter> output_files['output_selection'] and "file_gff3" in output_files['output_selection'] </filter> 177 <filter>output_files['output_selection'] and "file_gff3" in output_files['output_selection']</filter>
173 </data> 178 </data>
174 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff"> 179 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output/bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff">
175 <filter> output_files['output_selection'] and "file_gbff" in output_files['output_selection'] </filter> 180 <filter>output_files['output_selection'] and "file_gbff" in output_files['output_selection']</filter>
176 </data> 181 </data>
177 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl"> 182 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output/bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl">
178 <filter> output_files['output_selection'] and "file_embl" in output_files['output_selection'] </filter> 183 <filter>output_files['output_selection'] and "file_embl" in output_files['output_selection']</filter>
179 </data> 184 </data>
180 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences"> 185 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output/bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences">
181 <filter> output_files['output_selection'] and "file_fna" in output_files['output_selection'] </filter> 186 <filter>output_files['output_selection'] and "file_fna" in output_files['output_selection']</filter>
182 </data> 187 </data>
183 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences"> 188 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output/bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences">
184 <filter> output_files['output_selection'] and "file_ffn" in output_files['output_selection'] </filter> 189 <filter>output_files['output_selection'] and "file_ffn" in output_files['output_selection']</filter>
185 </data> 190 </data>
186 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences"> 191 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output/bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences">
187 <filter> output_files['output_selection'] and "file_faa" in output_files['output_selection'] </filter> 192 <filter>output_files['output_selection'] and "file_faa" in output_files['output_selection']</filter>
188 </data> 193 </data>
189 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary"> 194 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary">
190 <filter> output_files['output_selection'] and "hypo_tsv" in output_files['output_selection'] </filter> 195 <filter>output_files['output_selection'] and "hypo_tsv" in output_files['output_selection']</filter>
191 </data> 196 </data>
192 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences"> 197 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output/bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences">
193 <filter> output_files['output_selection'] and "hypo_fa" in output_files['output_selection'] </filter> 198 <filter>output_files['output_selection'] and "hypo_fa" in output_files['output_selection']</filter>
194 </data> 199 </data>
195 <data name="summary_txt" format="txt" from_work_dir="bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary"> 200 <data name="summary_txt" format="txt" from_work_dir="bakta_output/bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary">
196 <filter> output_files['output_selection'] and "sum_txt" in output_files['output_selection'] </filter> 201 <filter>output_files['output_selection'] and "sum_txt" in output_files['output_selection']</filter>
197 </data> 202 </data>
198 <data name="annotation_json" format="json" from_work_dir="bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable"> 203 <data name="annotation_json" format="json" from_work_dir="bakta_output/bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable">
199 <filter> output_files['output_selection'] and "file_json" in output_files['output_selection'] </filter> 204 <filter>output_files['output_selection'] and "file_json" in output_files['output_selection']</filter>
200 </data> 205 </data>
201 <data name="annotation_plot" format="svg" from_work_dir="bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation"> 206 <data name="annotation_plot" format="svg" from_work_dir="bakta_output/bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation">
202 <filter> output_files['output_selection'] and "file_plot" in output_files['output_selection'] </filter> 207 <filter>output_files['output_selection'] and "file_plot" in output_files['output_selection']</filter>
203 </data> 208 </data>
204 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> 209 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
205 <filter> output_files['output_selection'] and "log_txt" in output_files['output_selection'] </filter> 210 <filter>output_files['output_selection'] and "log_txt" in output_files['output_selection']</filter>
206 </data> 211 </data>
207 </outputs> 212 </outputs>
208 <tests> 213 <tests>
209 <test expect_num_outputs="13"> <!-- TEST_1 database + input --> 214 <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
210 <section name="input_option" > 215 <section name="input_option" >
211 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 216 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
212 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 217 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
213 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> 218 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
214 <param name="min_contig_length" value="250"/> 219 <param name="min_contig_length" value="250"/>
215 </section> 220 </section>
216 <section name="output_files"> 221 <section name="output_files">
224 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/> 229 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
225 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/> 230 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
226 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/> 231 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
227 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/> 232 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
228 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/> 233 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
229 <output name="annotation_plot"> 234 <output name="annotation_plot" value="TEST_1/TEST_1_plot.svg" ftype="svg" compare="sim_size"/>
230 <assert_contents>
231 <has_size value="418991" delta="1000"/>
232 </assert_contents>
233 </output>
234 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/> 235 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
235 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/> 236 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="15"/>
236 </test> 237 </test>
237 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> 238 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps -->
238 <section name="input_option" > 239 <section name="input_option" >
239 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 240 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
240 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 241 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
241 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> 242 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
242 <param name="min_contig_length" value="250"/> 243 <param name="min_contig_length" value="250"/>
243 </section> 244 </section>
244 <section name="organism"> 245 <section name="organism">
262 <assert_contents> 263 <assert_contents>
263 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> 264 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/>
264 </assert_contents> 265 </assert_contents>
265 </output> 266 </output>
266 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> 267 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/>
267 <output name="annotation_plot"> 268 <output name="annotation_plot" value="TEST_2/TEST_2_plot.svg" ftype="svg" compare="sim_size"/>
268 <assert_contents>
269 <has_size value="418991" delta="1000"/>
270 </assert_contents>
271 </output>
272 </test> 269 </test>
273 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps --> 270 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps -->
274 <section name="input_option" > 271 <section name="input_option" >
275 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 272 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
276 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 273 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
277 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> 274 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
278 <param name="min_contig_length" value="350"/> 275 <param name="min_contig_length" value="350"/>
279 </section> 276 </section>
280 <section name="workflow"> 277 <section name="workflow">
281 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori"/> 278 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>
282 </section> 279 </section>
283 <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/> 280 <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/>
284 <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/> 281 <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/>
285 <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/> 282 <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/>
286 <output name="annotation_plot">
287 <assert_contents>
288 <has_size value="418399" delta="1000"/>
289 </assert_contents>
290 </output>
291 </test> 283 </test>
292 <test expect_num_outputs="4"> <!-- TEST_4 annotations --> 284 <test expect_num_outputs="4"> <!-- TEST_4 annotations -->
293 <section name="input_option" > 285 <section name="input_option" >
294 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 286 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
295 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 287 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
296 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> 288 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
297 </section> 289 </section>
298 <section name="annotation"> 290 <section name="annotation">
299 <param name="complete" value="true"/> 291 <param name="complete" value="true"/>
304 <param name="proteins" value="user-proteins.faa" ftype="fasta"/> 296 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
305 </section> 297 </section>
306 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/> 298 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>
307 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/> 299 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
308 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/> 300 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>
309 <output name="annotation_plot"> 301 <output name="annotation_plot" value="TEST_4/TEST_4_plot.svg" ftype="svg" compare="sim_size"/>
310 <assert_contents>
311 <has_size value="418399" delta="1000"/>
312 </assert_contents>
313 </output>
314 </test> 302 </test>
315 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary --> 303 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->
316 <section name="input_option" > 304 <section name="input_option" >
317 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 305 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
318 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 306 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
319 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> 307 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
320 </section> 308 </section>
321 <section name="annotation"> 309 <section name="annotation">
322 <param name="complete" value="true"/> 310 <param name="complete" value="true"/>
323 <param name="translation_table" value="4"/> 311 <param name="translation_table" value="4"/>
324 </section> 312 </section>
325 <section name="workflow"> 313 <section name="workflow">
326 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori"/> 314 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>
327 </section> 315 </section>
328 <section name="output_files"> 316 <section name="output_files">
329 <param name="output_selection" value="log_txt,sum_txt"/> 317 <param name="output_selection" value="log_txt,sum_txt"/>
330 </section> 318 </section>
331 <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/> 319 <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="13"/>
332 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/> 320 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>
333 </test> 321 </test>
322 <test expect_num_outputs="13"> <!-- TEST_6 metagenome option -->
323 <section name="input_option" >
324 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
325 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
326 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
327 </section>
328 <section name="annotation">
329 <param name="meta" value="true"/>
330 </section>
331 <section name="output_files">
332 <param name="output_selection" value="file_tsv,file_gff3,file_gbff,file_embl,file_fna,file_ffn,file_faa,hypo_tsv,hypo_fa,sum_txt,file_json,file_plot,log_txt"/>
333 </section>
334 <output name="annotation_tsv" value="TEST_6/TEST_6.tsv" lines_diff="2"/>
335 <output name="annotation_gff3" value="TEST_6/TEST_6.gff3" lines_diff="2"/>
336 <output name="annotation_gbff" value="TEST_6/TEST_6.gbff" lines_diff="8"/>
337 <output name="annotation_embl" value="TEST_6/TEST_6.embl" lines_diff="6"/>
338 <output name="annotation_fna" value="TEST_6/TEST_6.fna"/>
339 <output name="annotation_ffn" value="TEST_6/TEST_6.ffn"/>
340 <output name="annotation_faa" value="TEST_6/TEST_6.faa"/>
341 <output name="hypotheticals_tsv" value="TEST_6/TEST_6.hypotheticals.tsv" lines_diff="4"/>
342 <output name="hypotheticals_faa" value="TEST_6/TEST_6.hypotheticals.faa"/>
343 <output name="summary_txt" value="TEST_6/TEST_6.txt" lines_diff="4"/>
344 <output name="annotation_plot" value="TEST_6/TEST_6_plot.svg" ftype="svg" compare="sim_size"/>
345 <output name="annotation_json" value="TEST_6/TEST_6.json" lines_diff="6"/>
346 <output name="logfile" value="TEST_6/TEST_6.log" lines_diff="15"/>
347 </test>
334 </tests> 348 </tests>
335 <help><![CDATA[**What it does** 349 <help><![CDATA[**What it does**
336 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. 350 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.
337 351
338 *Comprehensive & taxonomy-independent database* 352 *Comprehensive & taxonomy-independent database*