# HG changeset patch
# User iuc
# Date 1694854899 0
# Node ID 728dacaf08a94c1e90b8e0779581d90f935d6dae
# Parent  3f0aa1b3e816c60c705779b2663eaaf9cc7cdf82
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55

diff -r 3f0aa1b3e816 -r 728dacaf08a9 bakta.xml
--- a/bakta.xml	Mon Jul 24 11:22:16 2023 +0000
+++ b/bakta.xml	Sat Sep 16 09:01:39 2023 +0000
@@ -212,139 +212,145 @@
     </outputs>
     <tests>
         <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
-           <section name="input_option" >
-               <param name="bakta_db_select" value="V5.0_2022-08-19"/>
-               <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
-               <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" value="TEST_1/TEST_1_plot.svg" ftype="svg" compare="sim_size"/>
-          <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
-          <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="15"/>
-       </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="V5.0_2022-08-19"/>
-               <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
-               <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="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" value="TEST_2/TEST_2_plot.svg" ftype="svg" compare="sim_size"/>
-       </test>
-       <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps  -->
-           <section name="input_option" >
-               <param name="bakta_db_select" value="V5.0_2022-08-19"/>
-               <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-               <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
-               <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,--skip-plot"/>
-           </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"/>
-         </test>
-         <test expect_num_outputs="4"> <!-- TEST_4 annotations   -->
-             <section name="input_option" >
-                 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
-                 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
-             </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" ftype="tabular"/>
-                 <param name="compliant" value="true"/>
-                 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
-             </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" value="TEST_4/TEST_4_plot.svg" ftype="svg" compare="sim_size"/>
-         </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="V5.0_2022-08-19"/>
-                 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
-                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
-             </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,--skip-plot"/>
-             </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="13"/>
-             <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>
-         </test>
-         <test expect_num_outputs="13"> <!-- TEST_6 metagenome option -->
+            <section name="input_option" >
+                <param name="bakta_db_select" value="V5.0_2022-08-19"/>
+                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
+                <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
+                <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" value="TEST_1/TEST_1_plot.svg" ftype="svg" compare="sim_size"/>
+            <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
+            <output name="logfile" ftype="txt">
+                <expand macro="assert_content_test"/>
+            </output>
+        </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="V5.0_2022-08-19"/>
+                <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
+                <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
+                <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="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" value="TEST_2/TEST_2_plot.svg" ftype="svg" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps  -->
             <section name="input_option" >
                 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
                 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
                 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
+                <param name="min_contig_length" value="350"/>
             </section>
-            <section name="annotation">
-                <param name="meta" value="true"/>
-            </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 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,--skip-plot"/>
             </section>
-            <output name="annotation_tsv" value="TEST_6/TEST_6.tsv" lines_diff="2"/>
-            <output name="annotation_gff3" value="TEST_6/TEST_6.gff3" lines_diff="2"/>
-            <output name="annotation_gbff" value="TEST_6/TEST_6.gbff" lines_diff="8"/>
-            <output name="annotation_embl" value="TEST_6/TEST_6.embl" lines_diff="6"/>
-            <output name="annotation_fna" value="TEST_6/TEST_6.fna"/>
-            <output name="annotation_ffn" value="TEST_6/TEST_6.ffn"/>
-            <output name="annotation_faa" value="TEST_6/TEST_6.faa"/>
-            <output name="hypotheticals_tsv" value="TEST_6/TEST_6.hypotheticals.tsv" lines_diff="4"/>
-            <output name="hypotheticals_faa" value="TEST_6/TEST_6.hypotheticals.faa"/>
-            <output name="summary_txt" value="TEST_6/TEST_6.txt" lines_diff="4"/>
-            <output name="annotation_plot" value="TEST_6/TEST_6_plot.svg" ftype="svg" compare="sim_size"/>
-           <output name="annotation_json" value="TEST_6/TEST_6.json" lines_diff="6"/>
-           <output name="logfile" value="TEST_6/TEST_6.log" lines_diff="15"/>
-        </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"/>
+            </test>
+            <test expect_num_outputs="4"> <!-- TEST_4 annotations   -->
+                <section name="input_option" >
+                    <param name="bakta_db_select" value="V5.0_2022-08-19"/>
+                    <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
+                    <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
+                </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" ftype="tabular"/>
+                    <param name="compliant" value="true"/>
+                    <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
+                </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" value="TEST_4/TEST_4_plot.svg" ftype="svg" compare="sim_size"/>
+            </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="V5.0_2022-08-19"/>
+                    <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
+                    <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
+                </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,--skip-plot"/>
+                </section>
+                <section name="output_files">
+                    <param name="output_selection" value="log_txt,sum_txt"/>
+                </section>
+                <output name="logfile" ftype="txt">
+                    <expand macro="assert_content_test"/>
+                </output>
+                <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>
+            </test>
+            <test expect_num_outputs="13"> <!-- TEST_6 metagenome option -->
+                <section name="input_option" >
+                    <param name="bakta_db_select" value="V5.0_2022-08-19"/>
+                    <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
+                    <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
+                </section>
+                <section name="annotation">
+                    <param name="meta" value="true"/>
+                </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_6/TEST_6.tsv" lines_diff="2"/>
+                <output name="annotation_gff3" value="TEST_6/TEST_6.gff3" lines_diff="2"/>
+                <output name="annotation_gbff" value="TEST_6/TEST_6.gbff" lines_diff="8"/>
+                <output name="annotation_embl" value="TEST_6/TEST_6.embl" lines_diff="6"/>
+                <output name="annotation_fna" value="TEST_6/TEST_6.fna"/>
+                <output name="annotation_ffn" value="TEST_6/TEST_6.ffn"/>
+                <output name="annotation_faa" value="TEST_6/TEST_6.faa"/>
+                <output name="hypotheticals_tsv" value="TEST_6/TEST_6.hypotheticals.tsv" lines_diff="4"/>
+                <output name="hypotheticals_faa" value="TEST_6/TEST_6.hypotheticals.faa"/>
+                <output name="summary_txt" value="TEST_6/TEST_6.txt" lines_diff="4"/>
+                <output name="annotation_plot" value="TEST_6/TEST_6_plot.svg" ftype="svg" compare="sim_size"/>
+                <output name="annotation_json" value="TEST_6/TEST_6.json" lines_diff="6"/>
+                <output name="logfile" ftype="txt">
+                    <expand macro="assert_content_test"/>
+                </output>
+            </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.
diff -r 3f0aa1b3e816 -r 728dacaf08a9 macro.xml
--- a/macro.xml	Mon Jul 24 11:22:16 2023 +0000
+++ b/macro.xml	Sat Sep 16 09:01:39 2023 +0000
@@ -1,8 +1,8 @@
 
 <macros>
-    <token name="@TOOL_VERSION@">1.8.1</token>
+    <token name="@TOOL_VERSION@">1.8.2</token>
     <token name="@COMPATIBLE_BAKTA_VERSION@">1.7</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
         <version_command><![CDATA[bakta --version]]></version_command>
@@ -27,4 +27,15 @@
             <citation type="doi">10.1099/mgen.0.000685</citation>
         </citations>
     </xml>
+
+    <xml name="assert_content_test">
+        <assert_contents>
+            <has_text text="Options and arguments"/>
+            <has_text text="parse genome sequences"/>
+            <has_text text="start annotation"/>
+            <has_text text="genome statistics"/>
+            <has_text text="annotation summary"/>
+            <has_text text="export annotation results to"/>
+         </assert_contents>    
+    </xml>
 </macros>
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_1/TEST_1.gff3
--- a/test-data/TEST_1/TEST_1.gff3	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.gff3	Sat Sep 16 09:01:39 2023 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_1/TEST_1.hypotheticals.tsv
--- a/test-data/TEST_1/TEST_1.hypotheticals.tsv	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv	Sat Sep 16 09:01:39 2023 +0000
@@ -1,4 +1,4 @@
-#Annotated with Bakta v1.8.1, https://github.com/oschwengers/bakta
+#Annotated with Bakta v1.8.2, https://github.com/oschwengers/bakta
 #Database v5.0, https://doi.org/10.5281/zenodo.4247252
 #Sequence Id	Start	Stop	Strand	Locus Tag	Mol Weight [kDa]	Iso El. Point	Pfam hits	Dbxrefs
 contig_1	413	736	+	IHHALP_00005	12.1	10.4		
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_1/TEST_1.log
--- a/test-data/TEST_1/TEST_1.log	Mon Jul 24 11:22:16 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-Bakta v1.8.1
-Options and arguments:
-	input: /tmp/tmp6wdeee6u/files/3/2/d/dataset_32d4899b-3214-49f6-a57b-29ff0e04425d.dat
-	db: /tmp/tmp6wdeee6u/job_working_directory/000/2/working/database_path, version 5.0, full
-	output: /tmp/tmp6wdeee6u/job_working_directory/000/2/working/bakta_output
-	tmp directory: /tmp/tmp6wdeee6u/tmp/tmpm3wbu37o
-	prefix: bakta_output
-	threads: 1
-	translation table: 11
-
-parse genome sequences...
-	imported: 1
-	filtered & revised: 1
-	plasmids: 1
-
-start annotation...
-predict tRNAs...
-	found: 0
-predict tmRNAs...
-	found: 0
-predict rRNAs...
-	found: 0
-predict ncRNAs...
-	found: 0
-predict ncRNA regions...
-	found: 0
-predict CRISPR arrays...
-	found: 0
-predict & annotate CDSs...
-	predicted: 2 
-	discarded spurious: 0
-	revised translational exceptions: 0
-	detected IPSs: 0
-	found PSCs: 0
-	found PSCCs: 0
-	lookup annotations...
-	conduct expert systems...
-		amrfinder: 0
-		protein sequences: 0
-	combine annotations and mark hypotheticals...
-	detect pseudogenes...
-		pseudogene candidates: 0
-		found pseudogenes: 0
-analyze hypothetical proteins: 2
-	detected Pfam hits: 0 
-	calculated proteins statistics
-	revise special cases...
-extract sORF...
-	potential: 22
-	discarded due to overlaps: 2
-	discarded spurious: 0
-	detected IPSs: 0
-	found PSCs: 0
-	lookup annotations...
-	filter and combine annotations...
-	filtered sORFs: 0
-detect gaps...
-	found: 0
-detect oriCs/oriVs...
-	found: 0
-detect oriTs...
-	found: 0
-apply feature overlap filters...
-select features and create locus tags...
-selected: 2
-improve annotations...
-	revised gene symbols: 0
-
-genome statistics:
-	Genome size: 1,330 bp
-	Contigs/replicons: 1
-	GC: 45.2 %
-	N50: 1,330
-	N ratio: 0.0 %
-	coding density: 62.0 %
-
-annotation summary:
-	tRNAs: 0
-	tmRNAs: 0
-	rRNAs: 0
-	ncRNAs: 0
-	ncRNA regions: 0
-	CRISPR arrays: 0
-	CDSs: 2
-		hypotheticals: 2
-		pseudogenes: 0
-		signal peptides: 0
-	sORFs: 0
-	gaps: 0
-	oriCs/oriVs: 0
-	oriTs: 0
-
-export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/2/working/bakta_output
-	human readable TSV...
-	GFF3...
-	INSDC GenBank & EMBL...
-	genome sequences...
-	feature nucleotide sequences...
-	translated CDS sequences...
-	circular genome plot...
-	hypothetical TSV...
-	translated hypothetical CDS sequences...
-	machine readable JSON...
-	genome and annotation summary...
-
-If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685
-Annotation successfully finished in 0:01 [mm:ss].
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_1/TEST_1.tsv
--- a/test-data/TEST_1/TEST_1.tsv	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.tsv	Sat Sep 16 09:01:39 2023 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_1/TEST_1.txt
--- a/test-data/TEST_1/TEST_1.txt	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_1/TEST_1.txt	Sat Sep 16 09:01:39 2023 +0000
@@ -24,7 +24,7 @@
 oriTs: 0
 
 Bakta:
-Software: v1.8.1
+Software: v1.8.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_2/TEST_2.gff3
--- a/test-data/TEST_2/TEST_2.gff3	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_2/TEST_2.gff3	Sat Sep 16 09:01:39 2023 +0000
@@ -2,7 +2,7 @@
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # organism Escherichia coli o157:h7 Sakai
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_2/TEST_2.tsv
--- a/test-data/TEST_2/TEST_2.tsv	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_2/TEST_2.tsv	Sat Sep 16 09:01:39 2023 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_3/TEST_3.gff3
--- a/test-data/TEST_3/TEST_3.gff3	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_3/TEST_3.gff3	Sat Sep 16 09:01:39 2023 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_3/TEST_3.tsv
--- a/test-data/TEST_3/TEST_3.tsv	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_3/TEST_3.tsv	Sat Sep 16 09:01:39 2023 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_4/TEST_4.gff3
--- a/test-data/TEST_4/TEST_4.gff3	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_4/TEST_4.gff3	Sat Sep 16 09:01:39 2023 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_4/TEST_4.tsv
--- a/test-data/TEST_4/TEST_4.tsv	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_4/TEST_4.tsv	Sat Sep 16 09:01:39 2023 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_5/TEST_5.log
--- a/test-data/TEST_5/TEST_5.log	Mon Jul 24 11:22:16 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-Bakta v1.8.1
-Options and arguments:
-	input: /tmp/tmp6wdeee6u/files/0/2/9/dataset_0293aae0-943d-4d1b-af6c-e5ed41b419da.dat
-	db: /tmp/tmp6wdeee6u/job_working_directory/000/13/working/database_path, version 5.0, full
-	output: /tmp/tmp6wdeee6u/job_working_directory/000/13/working/bakta_output
-	tmp directory: /tmp/tmp6wdeee6u/tmp/tmpigp60rnb
-	prefix: bakta_output
-	threads: 1
-	translation table: 4
-	complete replicons: True
-	skip tRNA: True
-	skip tmRNA: True
-	skip rRNA: True
-	skip ncRNA: True
-	skip ncRNA region: True
-	skip CRISPR: True
-	skip CDS: True
-	skip sORF: True
-	skip gap: True
-	skip oriC/V/T: True
-	skip plot: True
-
-parse genome sequences...
-	imported: 1
-	filtered & revised: 1
-	plasmids: 1
-
-start annotation...
-skip tRNA prediction...
-skip tmRNA prediction...
-skip rRNA prediction...
-skip ncRNA prediction...
-skip ncRNA region prediction...
-skip CRISPR array prediction...
-skip CDS prediction...
-skip sORF prediction...
-skip gap annotation...
-skip oriC/T annotation...
-apply feature overlap filters...
-select features and create locus tags...
-selected: 0
-improve annotations...
-	revised gene symbols: 0
-
-genome statistics:
-	Genome size: 1,330 bp
-	Contigs/replicons: 1
-	GC: 45.2 %
-	N50: 1,330
-	N ratio: 0.0 %
-	coding density: 0.0 %
-
-annotation summary:
-	tRNAs: 0
-	tmRNAs: 0
-	rRNAs: 0
-	ncRNAs: 0
-	ncRNA regions: 0
-	CRISPR arrays: 0
-	CDSs: 0
-		hypotheticals: 0
-		pseudogenes: 0
-		signal peptides: 0
-	sORFs: 0
-	gaps: 0
-	oriCs/oriVs: 0
-	oriTs: 0
-
-export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/13/working/bakta_output
-	human readable TSV...
-	GFF3...
-	INSDC GenBank & EMBL...
-	genome sequences...
-	feature nucleotide sequences...
-	translated CDS sequences...
-	skip generation of circular genome plot...
-	machine readable JSON...
-	genome and annotation summary...
-
-If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685
-Annotation successfully finished in 0:00 [mm:ss].
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_5/TEST_5.txt
--- a/test-data/TEST_5/TEST_5.txt	Mon Jul 24 11:22:16 2023 +0000
+++ b/test-data/TEST_5/TEST_5.txt	Sat Sep 16 09:01:39 2023 +0000
@@ -24,7 +24,7 @@
 oriTs: 0
 
 Bakta:
-Software: v1.8.1
+Software: v1.8.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta
diff -r 3f0aa1b3e816 -r 728dacaf08a9 test-data/TEST_6/TEST_6.log
--- a/test-data/TEST_6/TEST_6.log	Mon Jul 24 11:22:16 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-Bakta v1.8.1
-Options and arguments:
-	input: /tmp/tmp6wdeee6u/files/4/2/7/dataset_4276a0b6-bcea-42e6-a1e2-9f880300f5a1.dat
-	db: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/database_path, version 5.0, full
-	output: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/bakta_output
-	tmp directory: /tmp/tmp6wdeee6u/tmp/tmpkzvj8z8k
-	prefix: bakta_output
-	threads: 1
-	translation table: 11
-
-parse genome sequences...
-	imported: 1
-	filtered & revised: 1
-	plasmids: 1
-
-start annotation...
-predict tRNAs...
-	found: 0
-predict tmRNAs...
-	found: 0
-predict rRNAs...
-	found: 0
-predict ncRNAs...
-	found: 0
-predict ncRNA regions...
-	found: 0
-predict CRISPR arrays...
-	found: 0
-predict & annotate CDSs...
-	predicted: 2 
-	discarded spurious: 0
-	revised translational exceptions: 0
-	detected IPSs: 0
-	found PSCs: 0
-	found PSCCs: 0
-	lookup annotations...
-	conduct expert systems...
-		amrfinder: 0
-		protein sequences: 0
-	combine annotations and mark hypotheticals...
-	detect pseudogenes...
-		pseudogene candidates: 0
-		found pseudogenes: 0
-analyze hypothetical proteins: 2
-	detected Pfam hits: 0 
-	calculated proteins statistics
-	revise special cases...
-extract sORF...
-	potential: 22
-	discarded due to overlaps: 2
-	discarded spurious: 0
-	detected IPSs: 0
-	found PSCs: 0
-	lookup annotations...
-	filter and combine annotations...
-	filtered sORFs: 0
-detect gaps...
-	found: 0
-detect oriCs/oriVs...
-	found: 0
-detect oriTs...
-	found: 0
-apply feature overlap filters...
-select features and create locus tags...
-selected: 2
-improve annotations...
-	revised gene symbols: 0
-
-genome statistics:
-	Genome size: 1,330 bp
-	Contigs/replicons: 1
-	GC: 45.2 %
-	N50: 1,330
-	N ratio: 0.0 %
-	coding density: 62.0 %
-
-annotation summary:
-	tRNAs: 0
-	tmRNAs: 0
-	rRNAs: 0
-	ncRNAs: 0
-	ncRNA regions: 0
-	CRISPR arrays: 0
-	CDSs: 2
-		hypotheticals: 2
-		pseudogenes: 0
-		signal peptides: 0
-	sORFs: 0
-	gaps: 0
-	oriCs/oriVs: 0
-	oriTs: 0
-
-export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/bakta_output
-	human readable TSV...
-	GFF3...
-	INSDC GenBank & EMBL...
-	genome sequences...
-	feature nucleotide sequences...
-	translated CDS sequences...
-	circular genome plot...
-	hypothetical TSV...
-	translated hypothetical CDS sequences...
-	machine readable JSON...
-	genome and annotation summary...
-
-If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685
-Annotation successfully finished in 0:01 [mm:ss].