Mercurial > repos > iuc > bakta
diff bakta.xml @ 2:debdc1469b41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
| author | iuc |
|---|---|
| date | Wed, 21 Dec 2022 20:59:54 +0000 |
| parents | da5f1924bb2e |
| children | 865ece5ca178 |
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--- a/bakta.xml Fri Sep 16 13:42:15 2022 +0000 +++ b/bakta.xml Wed Dec 21 20:59:54 2022 +0000 @@ -11,6 +11,10 @@ <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ + mkdir ./database_path && + ln -s '$(input_option.bakta_db_select.fields.path)/'* database_path && + ln -s '$(input_option.amrfinder_db_select.fields.path)' database_path && + bakta #*====================================== CPU option @@ -19,7 +23,7 @@ #*====================================== Bakta database ======================================*# - --db $input_option.db_select.fields.path + --db ./database_path #if $input_option.min_contig_length --min-contig-length $input_option.min_contig_length #else if $annotation.compliant @@ -71,36 +75,7 @@ skip some step of the bakta analysis ======================================*# - #if "skip_trna" in $workflow.skip_analysis - --skip-trna - #end if - #if "skip_tmrna" in $workflow.skip_analysis - --skip-tmrna - #end if - #if "skip_rrna" in $workflow.skip_analysis - --skip-rrna - #end if - #if "skip_ncrna" in $workflow.skip_analysis - --skip-ncrna - #end if - #if "skip_ncrna_region" in $workflow.skip_analysis - --skip-ncrna-region - #end if - #if "skip_crispr" in $workflow.skip_analysis - --skip-crispr - #end if - #if "skip_cds" in $workflow.skip_analysis - --skip-cds - #end if - #if "skip_sorf" in $workflow.skip_analysis - --skip-sorf - #end if - #if "skip_gap" in $workflow.skip_analysis - --skip-gap - #end if - #if "skip_ori" in $workflow.skip_analysis - --skip-ori - #end if + #echo " ".join($workflow.skip_analysis) #*====================================== Genome file @@ -114,11 +89,18 @@ <inputs> <!-- DB and file INPUT --> <section name="input_option" title="Input/Output options" expanded="true"> - <param name="db_select" type="select" label="The bakta database"> + <param name="bakta_db_select" type="select" label="The bakta database"> <options from_data_table="bakta_database"> - <validator message="No bakta database is available" type="no_options"/> + <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/> + <validator message="No bakta database is available" type="no_options"/> </options> </param> + <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> + <options from_data_table="amrfinderplus_database"> + <validator message="No amrfinderplus database is available" type="no_options"/> + </options> + </param> + <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/> <param name="min_contig_length" type="integer" optional="true" min="0" label="Minimum contig size" help="Minimum contig size (default = 1; 200 in compliant mode) (--min-contig-length)"/> </section> @@ -158,41 +140,43 @@ <!-- PARAMETER FOR WORKFLOW ANALYSIS --> <section name="workflow" title="Workflow option to skip steps"> <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip"> - <option value="skip_trna"> Skip tRNA detection and annotation </option> - <option value="skip_tmrna"> Skip tmRNA detection and annotation </option> - <option value="skip_rrna"> Skip rRNA detection and annotation </option> - <option value="skip_ncrna"> Skip ncRNA detection and annotation </option> - <option value="skip_ncrna_region"> Skip ncRNA region detection and annotation </option> - <option value="skip_crispr"> Skip CRISPR array detection and annotation </option> - <option value="skip_cds"> Skip CDS detection and annotation </option> - <option value="skip_sorf"> Skip sORF detection and annotation </option> - <option value="skip_gap"> Skip gap detection and annotation </option> - <option value="skip_ori"> Skip oriC/oriT detection and annotation </option> + <option value="--skip-trna"> Skip tRNA detection and annotation </option> + <option value="--skip-tmrna"> Skip tmRNA detection and annotation </option> + <option value="--skip-rrna"> Skip rRNA detection and annotation </option> + <option value="--skip-ncrna"> Skip ncRNA detection and annotation </option> + <option value="--skip-ncrna-region"> Skip ncRNA region detection and annotation </option> + <option value="--skip-crispr"> Skip CRISPR array detection and annotation </option> + <option value="--skip-cds"> Skip CDS detection and annotation </option> + <option value="--skip-pseudo"> Skip pseudogene detection and annotation </option> + <option value="--skip-sorf"> Skip sORF detection and annotation </option> + <option value="--skip-gap"> Skip gap detection and annotation </option> + <option value="--skip-ori"> Skip oriC/oriT detection and annotation </option> </param> </section> <section name="output_files" title="Selection of the output files"> <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> <option value="file_tsv" selected="true"> Annotation file in TSV </option> <option value="file_gff3" selected="true"> Annotation and sequence in GFF3 </option> - <option value="file_gbff" selected="true"> Annotations and sequences in GenBank format </option> - <option value="file_embl" selected="true"> Annotations and sequences in EMBL format </option> - <option value="file_fna" selected="true"> Replicon/contig DNA sequences as FASTA </option> + <option value="file_gbff" selected="false"> Annotations and sequences in GenBank format </option> + <option value="file_embl" selected="false"> Annotations and sequences in EMBL format </option> + <option value="file_fna" selected="false"> Replicon/contig DNA sequences as FASTA </option> <option value="file_ffn" selected="true"> Feature nucleotide sequences as FASTA </option> - <option value="file_faa" selected="true"> CDS/sORF amino acid sequences as FASTA </option> - <option value="hypo_tsv" selected="true"> Hypothetical protein CDS in TSV</option> - <option value="hypo_fa" selected="true"> Hypothetical protein CDS amino sequences as FASTA</option> - <option value="sum_txt" selected="true"> Summary as TXT</option> - <option value="file_json" selected="true"> Information on each annotated feature as JSON </option> - <option value="log_txt" selected="true"> Log file as TXT </option> + <option value="file_faa" selected="false"> CDS/sORF amino acid sequences as FASTA </option> + <option value="hypo_tsv" selected="false"> Hypothetical protein CDS in TSV</option> + <option value="hypo_fa" selected="false"> Hypothetical protein CDS amino sequences as FASTA</option> + <option value="sum_txt" selected="false"> Summary as TXT</option> + <option value="file_json" selected="false"> Information on each annotated feature as JSON </option> + <option value="file_plot" selected="true"> Plot of the annotation result as SVG </option> + <option value="log_txt" selected="false"> Log file as TXT </option> </param> </section> </inputs> <outputs> - <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output.tsv" label="${tool.name} on ${on_string}: bakta_output.tsv"> + <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary"> <filter> output_files['output_selection'] and "file_tsv" in output_files['output_selection'] </filter> </data> - <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output.gff3" label="${tool.name} on ${on_string}: bakta_output.gff3"> + <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences"> <filter> output_files['output_selection'] and "file_gff3" in output_files['output_selection'] </filter> </data> <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff"> @@ -201,223 +185,162 @@ <data name="annotation_embl" format="tabular" from_work_dir="bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl"> <filter> output_files['output_selection'] and "file_embl" in output_files['output_selection'] </filter> </data> - <data name="annotation_fna" format="fasta" from_work_dir="bakta_output.fna" label="${tool.name} on ${on_string}: bakta_output.fna"> + <data name="annotation_fna" format="fasta" from_work_dir="bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences"> <filter> output_files['output_selection'] and "file_fna" in output_files['output_selection'] </filter> </data> - <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output.ffn" label="${tool.name} on ${on_string}: bakta_output.ffn"> + <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences"> <filter> output_files['output_selection'] and "file_ffn" in output_files['output_selection'] </filter> </data> - <data name="annotation_faa" format="fasta" from_work_dir="bakta_output.faa" label="${tool.name} on ${on_string}: bakta_output.faa"> + <data name="annotation_faa" format="fasta" from_work_dir="bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences"> <filter> output_files['output_selection'] and "file_faa" in output_files['output_selection'] </filter> </data> - <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: bakta_output.hypotheticals.tsv"> + <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary"> <filter> output_files['output_selection'] and "hypo_tsv" in output_files['output_selection'] </filter> </data> - <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: bakta_output.hypotheticals.faa"> + <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences"> <filter> output_files['output_selection'] and "hypo_fa" in output_files['output_selection'] </filter> </data> - <data name="summary_txt" format="txt" from_work_dir="bakta_output.txt" label="${tool.name} on ${on_string}: bakta_summary.txt"> + <data name="summary_txt" format="txt" from_work_dir="bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary"> <filter> output_files['output_selection'] and "sum_txt" in output_files['output_selection'] </filter> </data> - <data name="annotation_json" format="json" from_work_dir="bakta_output.json" label="${tool.name} on ${on_string}: bakta_output.json"> + <data name="annotation_json" format="json" from_work_dir="bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable"> <filter> output_files['output_selection'] and "file_json" in output_files['output_selection'] </filter> </data> + <data name="annotation_plot" format="svg" from_work_dir="bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation"> + <filter> output_files['output_selection'] and "file_plot" in output_files['output_selection'] </filter> + </data> <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> <filter> output_files['output_selection'] and "log_txt" in output_files['output_selection'] </filter> </data> </outputs> - <tests> - <test expect_num_outputs="12"> <!-- TEST_1 database + input --> - <section name="input_option" > - <param name="db_select" value="test-db-bakta"/> - <param name="input_file" value="NC_002127.1.fna"/> - </section> - <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="10"> - <assert_contents> - <has_text_matching n="1" expression="Genome size: 1,330 bp"/> - <has_n_lines n="94" delta="1"/> - </assert_contents> - </output> - <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="1"/> - <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"> - <assert_contents> - <has_text_matching expression="TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC"/> - </assert_contents> - </output> - <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="4"> - <assert_contents> - <has_text_matching expression="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA"/> - </assert_contents> - </output> - <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="2"/> - <output name="annotation_fna" value="TEST_1/TEST_1.fna"/> - <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/> - <output name="annotation_faa" value="TEST_1/TEST_1.faa"/> - <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv"/> - <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/> - <output name="summary_txt" value="TEST_1/TEST_1.txt"> - <assert_contents> - <has_text_matching expression="N50: 1330"/> - </assert_contents> + <test expect_num_outputs="13"> <!-- TEST_1 database + input --> + <section name="input_option" > + <param name="bakta_db_select" value="V0.1_2022-08-29"/> + <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> + <param name="input_file" value="NC_002127.1.fna"/> + <param name="min_contig_length" value="250"/> + </section> + <section name="output_files"> + <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"/> + </section> + <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/> + <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/> + <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/> + <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/> + <output name="annotation_fna" value="TEST_1/TEST_1.fna"/> + <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/> + <output name="annotation_faa" value="TEST_1/TEST_1.faa"/> + <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/> + <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/> + <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/> + <output name="annotation_plot"> + <assert_contents> + <has_size value="418991" delta="1000"/> + </assert_contents> </output> - <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="4"> - <assert_contents> - <has_text_matching expression="0.6203007518796992"/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="12"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> - <section name="input_option" > - <param name="db_select" value="test-db-bakta"/> - <param name="input_file" value="NC_002127.1.fna"/> - <param name="min_contig_length" value="250"/> - </section> - <section name="organism"> - <param name="genus" value="Escherichia"/> - <param name="species" value="coli O157:H7"/> - <param name="strain" value="Sakai"/> - <param name="plasmid" value="pOSAK1"/> - </section> - <section name="annotation"> - <param name="--gram" value="-"/> - <param name="keep_contig_headers" value="true"/> - </section> - <section name="workflow"> - <param name="skip_analysis" value="skip_trna,skip_tmrna"/> - </section> - <output name="logfile" value="TEST_2/TEST_2.log" lines_diff="4"> - <assert_contents> - <has_text_matching expression="Genome size: 1,330 bp"/> - </assert_contents> - </output> - <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="2"> - <assert_contents> - <has_text_matching expression="IHHALP_00005"/> - </assert_contents> - </output> - <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="2"> - <assert_contents> - <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> - </assert_contents> - </output> - <output name="annotation_gbff" value="TEST_2/TEST_2.gbff" lines_diff="5"> - <assert_contents> - <has_text_matching expression="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA"/> - </assert_contents> - </output> - <output name="annotation_embl" value="TEST_2/TEST_2.embl" lines_diff="4"> - <assert_contents> - <has_text_matching expression="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA"/> - </assert_contents> - </output> - <output name="annotation_fna" value="TEST_2/TEST_2.fna"/> - <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> - <output name="annotation_faa" value="TEST_2/TEST_2.faa"/> - <output name="hypotheticals_tsv" value="TEST_2/TEST_2.hypotheticals.tsv"/> - <output name="hypotheticals_faa" value="TEST_2/TEST_2.hypotheticals.faa"/> - <output name="summary_txt" value="TEST_2/TEST_2.txt"> - <assert_contents> - <has_text_matching expression="N50: 1330"/> - </assert_contents> - </output> - <output name="annotation_json" value="TEST_2/TEST_2.json" lines_diff="4"> - <assert_contents> - <has_text_matching expression="0.4518796992481203"/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="12"> <!-- TEST_3 test all skip steps --> - <section name="input_option" > - <param name="db_select" value="test-db-bakta"/> - <param name="input_file" value="NC_002127.1.fna"/> - <param name="min_contig_length" value="350"/> - </section> - <section name="workflow"> - <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"/> - </section> - <output name="logfile" value="TEST_3/TEST_3.log" lines_diff="4"> - <assert_contents> - <has_text_matching expression="Genome size: 1,330 bp"/> - </assert_contents> - </output> - <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="1"/> - <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="2"/> - <output name="annotation_gbff" value="TEST_3/TEST_3.gbff" lines_diff="10"/> - <output name="annotation_embl" value="TEST_3/TEST_3.embl" lines_diff="4"/> - <output name="annotation_fna" value="TEST_3/TEST_3.fna"/> - <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/> - <output name="annotation_faa" value="TEST_3/TEST_3.faa"/> - <output name="annotation_json" value="TEST_3/TEST_3.json" lines_diff="4"/> + + <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/> + <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/> </test> - <test expect_num_outputs="12"> <!-- TEST_4 annotations --> + <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> <section name="input_option" > - <param name="db_select" value="test-db-bakta"/> + <param name="bakta_db_select" value="V0.1_2022-08-29"/> + <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> <param name="input_file" value="NC_002127.1.fna"/> + <param name="min_contig_length" value="250"/> + </section> + <section name="organism"> + <param name="genus" value="Escherichia"/> + <param name="species" value="coli O157:H7"/> + <param name="strain" value="Sakai"/> + <param name="plasmid" value="pOSAK1"/> </section> <section name="annotation"> - <param name="complete" value="true"/> - <param name="translation_table" value="4"/> - <param name="prodigal" value="prodigal.tf"/> - <param name="replicons" value="replicons.tsv"/> - <param name="compliant" value="true"/> - <param name="proteins" value="user-proteins.faa"/> + <param name="--gram" value="-"/> + <param name="keep_contig_headers" value="true"/> </section> - <output name="logfile" value="TEST_4/TEST_4.log" lines_diff="4"> + <section name="workflow"> + <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/> + </section> + <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4"> <assert_contents> - <has_text_matching expression="potential: 16"/> - </assert_contents> - </output> - <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="2"/> - <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="2"> - <assert_contents> - <has_text_matching expression="ID=IHHALP_00005_gene;locus_tag=IHHALP_00005"/> + <has_text_matching expression="IHHALP_00005"/> </assert_contents> </output> - <output name="annotation_gbff" value="TEST_4/TEST_4.gbff" lines_diff="4"> + <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4"> <assert_contents> - <has_text_matching expression="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA"/> - </assert_contents> - </output> - <output name="annotation_embl" value="TEST_4/TEST_4.embl" lines_diff="4"> - <assert_contents> - <has_text_matching expression="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA"/> + <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> </assert_contents> </output> - <output name="annotation_fna" value="TEST_4/TEST_4.fna"/> - <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/> - <output name="annotation_faa" value="TEST_4/TEST_4.faa"/> - <output name="hypotheticals_tsv" value="TEST_4/TEST_4.hypotheticals.tsv"/> - <output name="hypotheticals_faa" value="TEST_4/TEST_4.hypotheticals.faa"/> - <output name="summary_txt" value="TEST_4/TEST_4.txt"> + <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> + <output name="annotation_plot"> <assert_contents> - <has_text_matching expression="GC: 45.2"/> - </assert_contents> - </output> - <output name="annotation_json" value="TEST_4/TEST_4.json" lines_diff="4"> - <assert_contents> - <has_text_matching expression="0.4518796992481203"/> + <has_size value="418991" delta="1000"/> </assert_contents> </output> </test> - <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary --> + <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps --> <section name="input_option" > - <param name="db_select" value="test-db-bakta"/> + <param name="bakta_db_select" value="V0.1_2022-08-29"/> + <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> <param name="input_file" value="NC_002127.1.fna"/> - </section> - <section name="annotation"> - <param name="complete" value="true"/> - <param name="translation_table" value="4"/> + <param name="min_contig_length" value="350"/> </section> <section name="workflow"> - <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"/> + <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"/> </section> - <section name="output_files"> - <param name="output_selection" value="log_txt,sum_txt"/> - </section> - <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="4"/> - <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/> - </test> + <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/> + <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/> + <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/> + <output name="annotation_plot"> + <assert_contents> + <has_size value="418399" delta="1000"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> <!-- TEST_4 annotations --> + <section name="input_option" > + <param name="bakta_db_select" value="V0.1_2022-08-29"/> + <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> + <param name="input_file" value="NC_002127.1.fna"/> + </section> + <section name="annotation"> + <param name="complete" value="true"/> + <param name="prodigal" value="prodigal.tf"/> + <param name="translation_table" value="4"/> + <param name="replicons" value="replicons.tsv"/> + <param name="compliant" value="true"/> + <param name="proteins" value="user-proteins.faa"/> + </section> + <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/> + <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/> + <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/> + <output name="annotation_plot"> + <assert_contents> + <has_size value="418399" delta="1000"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary --> + <section name="input_option" > + <param name="bakta_db_select" value="V0.1_2022-08-29"/> + <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> + <param name="input_file" value="NC_002127.1.fna"/> + </section> + <section name="annotation"> + <param name="complete" value="true"/> + <param name="translation_table" value="4"/> + </section> + <section name="workflow"> + <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"/> + </section> + <section name="output_files"> + <param name="output_selection" value="log_txt,sum_txt"/> + </section> + <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/> + <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/> + </test> </tests> <help><![CDATA[**What it does** Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. @@ -465,7 +388,7 @@ **Annotation options** 1. You can specify if all sequences (chromosome or plasmids) are complete or not - 2. You can add your own prodigal traingin file for CDS predictionœ + 2. You can add your own prodigal training file for CDS predictionœ 3. The translation table could be modified, default is the 11th for bacteria 4. You can specify if bacteria is gram -/+ or unknonw (default value unknow) 5. You can keep the name of contig present in the input file