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comparison bakta.xml @ 8:c75629db91ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 2479a339881bcd17ccefc0e13daab5b8f1e693af-dirty
author pimarin
date Mon, 23 Jan 2023 14:05:58 +0000
parents 63452ec27d36
children 8c7499c6f32a
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7:63452ec27d36 8:c75629db91ff
56 --prodigal-tf '$annotation.prodigal' 56 --prodigal-tf '$annotation.prodigal'
57 #end if 57 #end if
58 #if $annotation.translation_table 58 #if $annotation.translation_table
59 --translation-table '$annotation.translation_table' 59 --translation-table '$annotation.translation_table'
60 #end if 60 #end if
61 --gram '?'
61 $annotation.keep_contig_headers 62 $annotation.keep_contig_headers
62 #if $annotation.replicons 63 #if $annotation.replicons
63 --replicons '$annotation.replicons' 64 --replicons '$annotation.replicons'
64 #end if 65 #end if
65 $annotation.compliant 66 $annotation.compliant
91 <validator message="No bakta database is available" type="no_options"/> 92 <validator message="No bakta database is available" type="no_options"/>
92 </options> 93 </options>
93 </param> 94 </param>
94 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> 95 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
95 <options from_data_table="amrfinderplus_database"> 96 <options from_data_table="amrfinderplus_database">
96 <column name="value" index="0"/>
97 <validator message="No amrfinderplus database is available" type="no_options"/> 97 <validator message="No amrfinderplus database is available" type="no_options"/>
98 </options> 98 </options>
99 </param> 99 </param>
100 100
101 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/> 101 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/>
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>
219 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/> 219 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>
220 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/> 220 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>
221 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/> 221 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>
222 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/> 222 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
223 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/> 223 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
224 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/> 224 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
225 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/> 225 <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"/> 226 <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"/> 227 <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"/> 228 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
229 <output name="annotation_plot"> 229 <output name="annotation_plot">
230 <assert_contents> 230 <assert_contents>
231 <has_size value="418991" delta="1000"/> 231 <has_size value="418991" delta="1000"/>
232 </assert_contents> 232 </assert_contents>
233 </output> 233 </output>
234
235 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/> 234 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
236 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/> 235 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/>
237 </test> 236 </test>
238 <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 -->
239 <section name="input_option" > 238 <section name="input_option" >
379 378
380 **Annotation options** 379 **Annotation options**
381 1. You can specify if all sequences (chromosome or plasmids) are complete or not 380 1. You can specify if all sequences (chromosome or plasmids) are complete or not
382 2. You can add your own prodigal training file for CDS predictionœ 381 2. You can add your own prodigal training file for CDS predictionœ
383 3. The translation table could be modified, default is the 11th for bacteria 382 3. The translation table could be modified, default is the 11th for bacteria
384 4. You can specify if bacteria is gram -/+ or unknonw (not available in galaxy tool <= 1.6.1) 383 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)
385 5. You can keep the name of contig present in the input file 384 5. You can keep the name of contig present in the input file
386 6. You can specify your own replicon table as a TSV/CSV file 385 6. You can specify your own replicon table as a TSV/CSV file
387 7. The compliance option is for ready to submit annotation file to Public database 386 7. The compliance option is for ready to submit annotation file to Public database
388 as ENA, Genbank EMBL 387 as ENA, Genbank EMBL
389 8. You can specify a protein sequence file for annotation in GenBank or fasta formats 388 8. You can specify a protein sequence file for annotation in GenBank or fasta formats