Mercurial > repos > iuc > bakta
comparison bakta.xml @ 4:3f0aa1b3e816 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
author | iuc |
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date | Mon, 24 Jul 2023 11:22:16 +0000 |
parents | 865ece5ca178 |
children | 728dacaf08a9 |
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3:865ece5ca178 | 4:3f0aa1b3e816 |
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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* |