| Previous changeset 2:debdc1469b41 (2022-12-21) Next changeset 4:3f0aa1b3e816 (2023-07-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738 |
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modified:
bakta.xml test-data/TEST_1/TEST_1.log test-data/TEST_2/TEST_2.log test-data/TEST_3/TEST_3.log test-data/TEST_4/TEST_4.log test-data/TEST_5/TEST_5.log test-data/amrfinderplus_database.loc tool_data_table_conf.xml.test |
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added:
test-data/TEST_2/TEST_2.svg test-data/TEST_3/TEST_3.svg test-data/TEST_4/TEST_4.svg |
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removed:
test-data/TEST_2/TEST_2.faa test-data/TEST_2/TEST_2.fna test-data/TEST_2/TEST_2.hypotheticals.faa test-data/TEST_3/TEST_3.faa test-data/TEST_3/TEST_3.fna test-data/TEST_4/TEST_4.faa test-data/TEST_4/TEST_4.fna test-data/TEST_4/TEST_4.hypotheticals.faa |
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| diff -r debdc1469b41 -r 865ece5ca178 bakta.xml --- a/bakta.xml Wed Dec 21 20:59:54 2022 +0000 +++ b/bakta.xml Fri Feb 10 14:20:09 2023 +0000 |
| [ |
| b'@@ -1,6 +1,6 @@\n <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>\n- genome annotation via alignment-free sequence identification\n+ Genome annotation via alignment-free sequence identification\n </description>\n <macros>\n <import>macro.xml</import>\n@@ -11,10 +11,9 @@\n <expand macro="version_command"/>\n \n <command detect_errors="aggressive"><![CDATA[\n- mkdir ./database_path &&\n- ln -s \'$(input_option.bakta_db_select.fields.path)/\'* database_path &&\n- ln -s \'$(input_option.amrfinder_db_select.fields.path)\' database_path &&\n-\n+ mkdir -p ./database_path/amrfinderplus-db &&\n+ ln -s \'$(input_option.bakta_db_select.fields.path)\'/* database_path &&\n+ ln -s \'$(input_option.amrfinder_db_select.fields.path)/\' database_path/amrfinderplus-db/latest &&\n bakta\n #*======================================\n CPU option\n@@ -59,9 +58,7 @@\n #if $annotation.translation_table\n --translation-table \'$annotation.translation_table\'\n #end if\n- #if $annotation.gram\n- --gram \'$annotation.gram\'\n- #end if\n+ --gram \'?\'\n $annotation.keep_contig_headers\n #if $annotation.replicons\n --replicons \'$annotation.replicons\'\n@@ -127,13 +124,8 @@\n <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>\n </param>\n- <param argument="--gram" type="select" optional="true" label="Gram type for signal peptide predictions" help="Gram type +/- or unknown. Default: unknown">\n- <option value="+">Gram+</option>\n- <option value="-">Gram-</option>\n- <option value="?" selected="true">Unknown</option>\n- </param>\n <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>\n- <param argument="--replicons" type="data" format="tsv,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>\n+ <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>\n <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>\n <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>\n </section>\n@@ -215,18 +207,18 @@\n </outputs>\n <tests>\n <test expect_num_outputs="13"> <!-- TEST_1 database + input -->\n- <section name="input_option" >\n- <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n- <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n- <param name="input_file" value="NC_002127.1.fna"/>\n- <param name="min_contig_length" value="250"/>\n- </section>\n- <section name="output_files">\n- <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"/>\n- </section>\n- <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>\n- <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>\n- <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>\n+ <section name="input_option" >\n+ <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n+ <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n+ '..b' <param name="compliant" value="true"/>\n- <param name="proteins" value="user-proteins.faa"/>\n- </section>\n- <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>\n- <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>\n- <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>\n- <output name="annotation_plot">\n- <assert_contents>\n- <has_size value="418399" delta="1000"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->\n- <section name="input_option" >\n- <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n- <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n- <param name="input_file" value="NC_002127.1.fna"/>\n- </section>\n- <section name="annotation">\n- <param name="complete" value="true"/>\n- <param name="translation_table" value="4"/>\n- </section>\n- <section name="workflow">\n- <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"/>\n- </section>\n- <section name="output_files">\n- <param name="output_selection" value="log_txt,sum_txt"/>\n- </section>\n- <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/>\n- <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>\n- </test>\n+ <assert_contents>\n+ <has_size value="418399" delta="1000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->\n+ <section name="input_option" >\n+ <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n+ <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n+ <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>\n+ </section>\n+ <section name="annotation">\n+ <param name="complete" value="true"/>\n+ <param name="translation_table" value="4"/>\n+ </section>\n+ <section name="workflow">\n+ <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"/>\n+ </section>\n+ <section name="output_files">\n+ <param name="output_selection" value="log_txt,sum_txt"/>\n+ </section>\n+ <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/>\n+ <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>\n+ </test>\n </tests>\n <help><![CDATA[**What it does**\n Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.\n@@ -390,7 +380,7 @@\n 1. You can specify if all sequences (chromosome or plasmids) are complete or not\n 2. You can add your own prodigal training file for CDS prediction\xc5\x93\n 3. The translation table could be modified, default is the 11th for bacteria\n- 4. You can specify if bacteria is gram -/+ or unknonw (default value unknow)\n+ 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)\n 5. You can keep the name of contig present in the input file\n 6. You can specify your own replicon table as a TSV/CSV file\n 7. The compliance option is for ready to submit annotation file to Public database\n' |
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| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_1/TEST_1.log --- a/test-data/TEST_1/TEST_1.log Wed Dec 21 20:59:54 2022 +0000 +++ b/test-data/TEST_1/TEST_1.log Fri Feb 10 14:20:09 2023 +0000 |
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| @@ -85,6 +85,7 @@ genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... hypothetical TSV... translated hypothetical CDS sequences... machine readable JSON... |
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| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_2/TEST_2.faa --- a/test-data/TEST_2/TEST_2.faa Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_2/TEST_2.fna --- a/test-data/TEST_2/TEST_2.fna Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ ->NC_002127.1 Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG |
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| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_2/TEST_2.hypotheticals.faa --- a/test-data/TEST_2/TEST_2.hypotheticals.faa Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_2/TEST_2.log --- a/test-data/TEST_2/TEST_2.log Wed Dec 21 20:59:54 2022 +0000 +++ b/test-data/TEST_2/TEST_2.log Fri Feb 10 14:20:09 2023 +0000 |
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| @@ -83,6 +83,7 @@ genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... hypothetical TSV... translated hypothetical CDS sequences... machine readable JSON... |
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| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_2/TEST_2.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.svg Fri Feb 10 14:20:09 2023 +0000 |
| b |
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| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_3/TEST_3.fna --- a/test-data/TEST_3/TEST_3.fna Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,24 +0,0 @@ ->contig_1 [completeness=complete] [topology=circular] [gcode=11] -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_3/TEST_3.log --- a/test-data/TEST_3/TEST_3.log Wed Dec 21 20:59:54 2022 +0000 +++ b/test-data/TEST_3/TEST_3.log Fri Feb 10 14:20:09 2023 +0000 |
| b |
| @@ -49,6 +49,7 @@ genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... machine readable JSON... genome and annotation summary... |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_3/TEST_3.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.svg Fri Feb 10 14:20:09 2023 +0000 |
| b |
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| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_4/TEST_4.faa --- a/test-data/TEST_4/TEST_4.faa Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_4/TEST_4.fna --- a/test-data/TEST_4/TEST_4.fna Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,24 +0,0 @@ ->p2 [completeness=complete] [topology=circular] [gcode=4] [plasmid-name=pOSAK1] -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_4/TEST_4.hypotheticals.faa --- a/test-data/TEST_4/TEST_4.hypotheticals.faa Wed Dec 21 20:59:54 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_4/TEST_4.log --- a/test-data/TEST_4/TEST_4.log Wed Dec 21 20:59:54 2022 +0000 +++ b/test-data/TEST_4/TEST_4.log Fri Feb 10 14:20:09 2023 +0000 |
| b |
| @@ -86,6 +86,7 @@ genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... hypothetical TSV... translated hypothetical CDS sequences... machine readable JSON... |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_4/TEST_4.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.svg Fri Feb 10 14:20:09 2023 +0000 |
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| diff -r debdc1469b41 -r 865ece5ca178 test-data/TEST_5/TEST_5.log --- a/test-data/TEST_5/TEST_5.log Wed Dec 21 20:59:54 2022 +0000 +++ b/test-data/TEST_5/TEST_5.log Fri Feb 10 14:20:09 2023 +0000 |
| b |
| @@ -49,6 +49,7 @@ genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... machine readable JSON... genome and annotation summary... |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 test-data/amrfinderplus_database.loc --- a/test-data/amrfinderplus_database.loc Wed Dec 21 20:59:54 2022 +0000 +++ b/test-data/amrfinderplus_database.loc Fri Feb 10 14:20:09 2023 +0000 |
| b |
| @@ -4,5 +4,5 @@ # value, name, path # # for example -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db +amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db/latest +amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db/latest |
| b |
| diff -r debdc1469b41 -r 865ece5ca178 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Dec 21 20:59:54 2022 +0000 +++ b/tool_data_table_conf.xml.test Fri Feb 10 14:20:09 2023 +0000 |
| b |
| @@ -7,5 +7,6 @@ <table name="amrfinderplus_database" comment_char="#"> <columns>value, name, path</columns> <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> + </table> </tables> |
