Mercurial > repos > pimarin > bakta
diff bakta.xml @ 6:f77ebe2e4df0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit bd3e03930af39dc50e6640430256555851e7b096
| author | pimarin |
|---|---|
| date | Fri, 13 Jan 2023 13:02:33 +0000 |
| parents | 44fb905481f0 |
| children | 63452ec27d36 |
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--- a/bakta.xml Thu Jan 12 11:25:17 2023 +0000 +++ b/bakta.xml Fri Jan 13 13:02:33 2023 +0000 @@ -1,6 +1,6 @@ <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> - genome annotation via alignment-free sequence identification + Genome annotation via alignment-free sequence identification </description> <macros> <import>macro.xml</import> @@ -11,10 +11,9 @@ <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ - mkdir ./database_path && - ln -s '$(input_option.bakta_db_select.fields.path)/*' database_path && - ln -rs '$(input_option.amrfinder_db_select.fields.path)' database_path/latest && - + mkdir -p ./database_path/amrfinderplus-db && + ln -sr '$(input_option.bakta_db_select.fields.path)'/* database_path && + ln -sr '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest && bakta #*====================================== CPU option @@ -215,132 +214,132 @@ </outputs> <tests> <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> + <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="6"/> - <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/> - </test> - <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> - <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="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="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4"> - <assert_contents> - <has_text_matching expression="IHHALP_00005"/> - </assert_contents> - </output> - <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4"> - <assert_contents> - <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> - </assert_contents> - </output> - <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> + <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="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> + <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="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="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4"> + <assert_contents> + <has_text_matching expression="IHHALP_00005"/> + </assert_contents> + </output> + <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4"> + <assert_contents> + <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> + </assert_contents> + </output> + <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> + <output name="annotation_plot"> + <assert_contents> + <has_size value="418991" delta="1000"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps --> + <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="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="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="418991" delta="1000"/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps --> - <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="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="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> + <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.