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comparison bakta.xml @ 11:f93f54a21132 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit ed22b0f3b7b651e240154a08c9313585def1cfe5
author pimarin
date Mon, 13 Feb 2023 11:37:06 +0000
parents ed4bc0577be6
children
comparison
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10:ed4bc0577be6 11:f93f54a21132
86 <inputs> 86 <inputs>
87 <!-- DB and file INPUT --> 87 <!-- DB and file INPUT -->
88 <section name="input_option" title="Input/Output options" expanded="true"> 88 <section name="input_option" title="Input/Output options" expanded="true">
89 <param name="bakta_db_select" type="select" label="The bakta database"> 89 <param name="bakta_db_select" type="select" label="The bakta database">
90 <options from_data_table="bakta_database"> 90 <options from_data_table="bakta_database">
91 <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/> 91 <filter type="static_value" value="@BAKTA_VERSION@" column="2"/>
92 <validator message="No bakta database is available" type="no_options"/> 92 <validator message="No bakta database is available" type="no_options"/>
93 </options> 93 </options>
94 </param> 94 </param>
95 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> 95 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
96 <options from_data_table="amrfinderplus_database"> 96 <options from_data_table="amrfinderplus_database">
123 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11"> 123 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11">
124 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> 124 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
125 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option> 125 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>
126 </param> 126 </param>
127 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/> 127 <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="tsv,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> 128 <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"/> 129 <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"/> 130 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
131 </section> 131 </section>
132 <!-- PARAMETER FOR WORKFLOW ANALYSIS --> 132 <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
133 <section name="workflow" title="Workflow option to skip steps"> 133 <section name="workflow" title="Workflow option to skip steps">
208 <tests> 208 <tests>
209 <test expect_num_outputs="13"> <!-- TEST_1 database + input --> 209 <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
210 <section name="input_option" > 210 <section name="input_option" >
211 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 211 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
212 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 212 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
213 <param name="input_file" value="NC_002127.1.fna"/> 213 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
214 <param name="min_contig_length" value="250"/> 214 <param name="min_contig_length" value="250"/>
215 </section> 215 </section>
216 <section name="output_files"> 216 <section name="output_files">
217 <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"/> 217 <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"/>
218 </section> 218 </section>
236 </test> 236 </test>
237 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> 237 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps -->
238 <section name="input_option" > 238 <section name="input_option" >
239 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 239 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
240 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 240 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
241 <param name="input_file" value="NC_002127.1.fna"/> 241 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
242 <param name="min_contig_length" value="250"/> 242 <param name="min_contig_length" value="250"/>
243 </section> 243 </section>
244 <section name="organism"> 244 <section name="organism">
245 <param name="genus" value="Escherichia"/> 245 <param name="genus" value="Escherichia"/>
246 <param name="species" value="coli O157:H7"/> 246 <param name="species" value="coli O157:H7"/>
272 </test> 272 </test>
273 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps --> 273 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps -->
274 <section name="input_option" > 274 <section name="input_option" >
275 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 275 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
276 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 276 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
277 <param name="input_file" value="NC_002127.1.fna"/> 277 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
278 <param name="min_contig_length" value="350"/> 278 <param name="min_contig_length" value="350"/>
279 </section> 279 </section>
280 <section name="workflow"> 280 <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"/> 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"/>
282 </section> 282 </section>
291 </test> 291 </test>
292 <test expect_num_outputs="4"> <!-- TEST_4 annotations --> 292 <test expect_num_outputs="4"> <!-- TEST_4 annotations -->
293 <section name="input_option" > 293 <section name="input_option" >
294 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 294 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
295 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 295 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
296 <param name="input_file" value="NC_002127.1.fna"/> 296 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
297 </section> 297 </section>
298 <section name="annotation"> 298 <section name="annotation">
299 <param name="complete" value="true"/> 299 <param name="complete" value="true"/>
300 <param name="prodigal" value="prodigal.tf"/> 300 <param name="prodigal" value="prodigal.tf"/>
301 <param name="translation_table" value="4"/> 301 <param name="translation_table" value="4"/>
302 <param name="replicons" value="replicons.tsv"/> 302 <param name="replicons" value="replicons.tsv" ftype="tabular"/>
303 <param name="compliant" value="true"/> 303 <param name="compliant" value="true"/>
304 <param name="proteins" value="user-proteins.faa"/> 304 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
305 </section> 305 </section>
306 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/> 306 <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"/> 307 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
308 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/> 308 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>
309 <output name="annotation_plot"> 309 <output name="annotation_plot">
314 </test> 314 </test>
315 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary --> 315 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->
316 <section name="input_option" > 316 <section name="input_option" >
317 <param name="bakta_db_select" value="V0.1_2022-08-29"/> 317 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
318 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> 318 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
319 <param name="input_file" value="NC_002127.1.fna"/> 319 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
320 </section> 320 </section>
321 <section name="annotation"> 321 <section name="annotation">
322 <param name="complete" value="true"/> 322 <param name="complete" value="true"/>
323 <param name="translation_table" value="4"/> 323 <param name="translation_table" value="4"/>
324 </section> 324 </section>