| Next changeset 1:102852801457 (2024-08-26) |
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Commit message:
planemo upload for repository https://github.com/nick-youngblut/gtdb_to_taxdump commit 5b1dd7712b2ba62d2310b175dca45d39e8a804dc |
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added:
macros.xml ncbi-gtdb_map.xml test-data/gtdb_test.tsv test-data/gtdbtk_database_metadata_versioned.loc.test test-data/ncbi_test.tsv test-data/ncbi_test_prefix.tsv test-data/test-db/ar53_metadata_r214.tsv test-data/test-db/bac120_metadata_r214.tsv tool-data/gtdbtk_database_metadata_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r ab933d3c6057 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,22 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">gtdb_to_taxdump</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.1.9</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools"> + gtdb_to_taxdump + </xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.5281/zenodo.3696964</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r ab933d3c6057 ncbi-gtdb_map.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbi-gtdb_map.xml Sun Aug 25 14:55:35 2024 +0000 |
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| b'@@ -0,0 +1,180 @@\n+<tool id="ncbi_gtdb_map" name="NCBI-GTDB map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Map taxonomic classifications between the NCBI and GTDB taxonomies</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="biotools"/>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ mkdir output &&\n+\n+ #if $data.is_select == \'history\':\n+ #for $f in $files:\n+ ln -s \'$f\' \'$f.element_identifier\' &&\n+ #end for\n+ #else:\n+ ln -s \'$metadata.fields.path/bac\'* \'bac_meta.tsv\' &&\n+ ln -s \'$metadata.fields.path/ar\'* \'ar_meta.tsv\' &&\n+ #end if \n+\n+ ncbi-gtdb_map.py\n+ #if $mode == \'gtdb\':\n+ -q gtdb_taxonomy\n+ #end if\n+ \'${names}\'\n+ #if $data.is_select == \'history\':\n+ #for $f in $files:\n+ \'$f.element_identifier\'\n+ #end for\n+ #else: \n+ \'bac_meta.tsv\'\n+ \'ar_meta.tsv\'\n+ #end if\n+ --completeness ${completeness}\n+ --contamination ${contamination}\n+ --fraction ${fraction}\n+ --max-tips ${max_tips}\n+ --column ${column}\n+ ${header}\n+ #if $add_prefix.is_select == \'y\':\n+ -p \'${prefix}\'\n+ #end if\n+ ${no_prefix}\n+ -o output\n+ --procs \\${GALAXY_SLOTS:-8}\n+\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param name="names" type="data" format="tabular" label="File with the names" help="You can either have a file the NCBI names or the GTDB names"/>\n+ <conditional name="data">\n+ <param name="is_select" type="select" label="Use either a cached ncbi database or upload from history">\n+ <option value="cached">Cached database</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param name="metadata" type="select" label="Metadata version" help="Choose metadata version">\n+ <options from_data_table="gtdbtk_database_metadata_versioned">\n+ <validator message="No gtdb metadata is available" type="no_options"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="files" format="tabular" type="data" multiple="true" label="Input bacteria and archaea meatdata files here" help="When using this please input the metadata files uncompressed!"/>\n+ </when>\n+ </conditional>\n+ <param name="mode" type="select" label="Select the type of mapping" help="Choose if you want to map NCBI agaisnt GTDB or the other way around">\n+ <option value="ncbi">NCBI to GTDB</option>\n+ <option value="gtdb">GTDB to NCBI</option>\n+ </param>\n+ <param argument="--completeness" type="float" value="50.0" label="Completeness filter" help="Only include GTDB genomes who have bigger or equal CheckM completeness"/>\n+ <param argument="--contamination" type="float" value="5.0" label="Contamination filter" help="Only include GTDB genomes who have a smaller CheckM contamination"/>\n+ <param argument="--fraction" type="float" min="0.0" max="1.0" value="0.9" label="Homogeneity of LCA" help="Change the homogeneity of LCA in order to be used"/>\n+ <param argument="--max-tips" type="integer" value="100" min="1" label="Max. number of tips" help="Select the number of tips used for LCA determination"/>\n+ <param argument="--column" type="data_column" data_ref="names" label="Select the column with the names"/>\n+ <param argument="--header" type="boolean" truevalue="--header" falsevalue="" checked="false" label="Header row in the input" help="Check if the input file has a header to so the program will skip it"/>\n+ <conditional name="add_pre'..b' <test expect_num_outputs="1">\n+ <param name="mode" value="gtdb"/>\n+ <param name="names" value="gtdb_test.tsv"/>\n+ <conditional name="data">\n+ <param name="is_select" value="history"/>\n+ <param name="files" value="test-db/ar53_metadata_r214.tsv,test-db/bac120_metadata_r214.tsv"/>\n+ </conditional>\n+ <param name="completeness" value="1.0"/>\n+ <param name="contamination" value="1.0"/>\n+ <param name="fraction" value="0.2"/>\n+ <param name="max_tips" value="10"/>\n+ <param name="column" value="2"/>\n+ <output name="output_gtdb">\n+ <assert_contents>\n+ <has_n_lines n="6" delta="1"/>\n+ <has_text text="unclassified" n="3"/>\n+ <not_has_text text="test1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="mode" value="ncbi"/>\n+ <param name="names" value="ncbi_test.tsv"/>\n+ <conditional name="data">\n+ <param name="is_select" value="history"/>\n+ <param name="files" value="test-db/ar53_metadata_r214.tsv,test-db/bac120_metadata_r214.tsv"/>\n+ </conditional>\n+ <param name="no_prefix" value="true"/>\n+ <param name="column" value="1"/>\n+ <output name="output_ncbi">\n+ <assert_contents>\n+ <has_n_lines n="4" delta="1"/>\n+ <has_text text="Bacteroides thetaiotaomicron" n="2"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="mode" value="ncbi"/>\n+ <param name="names" value="ncbi_test_prefix.tsv"/>\n+ <conditional name="data">\n+ <param name="is_select" value="cached"/>\n+ <param name="metadata" value="test-gtdb"/>\n+ </conditional>\n+ <param name="header" value="true"/>\n+ <param name="column" value="1"/>\n+ <output name="output_ncbi">\n+ <assert_contents>\n+ <has_n_lines n="4" delta="1"/>\n+ <has_text text="s__Bacteroides thetaiotaomicron"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+ .. class:: infomark\n+\n+ **Where to download the metadata**\n+\n+ The metadata can be download from `GTDB <https://data.gtdb.ecogenomic.org/releases/>`_. If you want to use this tool to convert gtdb naming from a GTDB tool such as `gtdbtk classify_wf` use the corresponding GTDB release of the metadata. After download it dont forget to uncompressed it!\n+\n+ **What does this tool**\n+\n+ This tool was desinged to map the GTDB taxonomy to the NCBI taxonomy since both are using different ID systems.\n+ This means this tool map either GTDB names to the NCBI names or the other way around. If the names contain prefixes like *s__* the mapped name also will contain there corresponded prefix. If you use the names without prefix then the mapped names also don\'t contain the prefixes.\n+\n+ **Prefixes**\n+\n+ The prefixes stand for the taxonomic rank for example s__Bacteroides thetaiotaomicron. If you use them directly with in the file where you list the names which should be queried then you dont need the prefix option but if you use names without them you can either manully include them with the prefix option (read the help section there too) or you can use the tool without them but then you have to check the no-prefix option! This means when you use the no-prefix option s__Bacteroides thetaiotaomicron will not be used in this tool but Bacteroides thetaiotaomicron will work fine!\n+ \n+ ]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r ab933d3c6057 test-data/gtdb_test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtdb_test.tsv Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,4 @@ +test1 c__Bacteroidia +test1 s__Homo sapiens + Blank + Burkholderiales \ No newline at end of file |
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| diff -r 000000000000 -r ab933d3c6057 test-data/gtdbtk_database_metadata_versioned.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtdbtk_database_metadata_versioned.loc.test Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,2 @@ +#value name version path +test-gtdb Test bac 214 ${__HERE__}/test-db |
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| diff -r 000000000000 -r ab933d3c6057 test-data/ncbi_test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_test.tsv Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,3 @@ +Methanobrevibacter smithii test +methanosarcina Barkeri test +Bacteroides thetaiotaomicron test \ No newline at end of file |
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| diff -r 000000000000 -r ab933d3c6057 test-data/ncbi_test_prefix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_test_prefix.tsv Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,4 @@ +TEST HEADER!!!! +s__Methanobrevibacter smithii test +s__methanosarcina Barkeri test +s__Bacteroides thetaiotaomicron test \ No newline at end of file |
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| diff -r 000000000000 -r ab933d3c6057 test-data/test-db/bac120_metadata_r214.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/bac120_metadata_r214.tsv Sun Aug 25 14:55:35 2024 +0000 |
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| b'@@ -0,0 +1,722 @@\n+accession\tambiguous_bases\tcheckm_completeness\tcheckm_contamination\tcheckm_marker_count\tcheckm_marker_lineage\tcheckm_marker_set_count\tcheckm_strain_heterogeneity\tcoding_bases\tcoding_density\tcontig_count\tgc_count\tgc_percentage\tgenome_size\tgtdb_genome_representative\tgtdb_representative\tgtdb_taxonomy\tgtdb_type_designation_ncbi_taxa\tgtdb_type_designation_ncbi_taxa_sources\tgtdb_type_species_of_genus\tl50_contigs\tl50_scaffolds\tlongest_contig\tlongest_scaffold\tlsu_23s_contig_len\tlsu_23s_count\tlsu_23s_length\tlsu_23s_query_id\tlsu_5s_contig_len\tlsu_5s_count\tlsu_5s_length\tlsu_5s_query_id\tlsu_silva_23s_blast_align_len\tlsu_silva_23s_blast_bitscore\tlsu_silva_23s_blast_evalue\tlsu_silva_23s_blast_perc_identity\tlsu_silva_23s_blast_subject_id\tlsu_silva_23s_taxonomy\tmean_contig_length\tmean_scaffold_length\tmimag_high_quality\tmimag_low_quality\tmimag_medium_quality\tn50_contigs\tn50_scaffolds\tncbi_assembly_level\tncbi_assembly_name\tncbi_assembly_type\tncbi_bioproject\tncbi_biosample\tncbi_contig_count\tncbi_contig_n50\tncbi_country\tncbi_date\tncbi_genbank_assembly_accession\tncbi_genome_category\tncbi_genome_representation\tncbi_isolate\tncbi_isolation_source\tncbi_lat_lon\tncbi_molecule_count\tncbi_ncrna_count\tncbi_organism_name\tncbi_protein_count\tncbi_refseq_category\tncbi_rrna_count\tncbi_scaffold_count\tncbi_scaffold_l50\tncbi_scaffold_n50\tncbi_scaffold_n75\tncbi_scaffold_n90\tncbi_seq_rel_date\tncbi_spanned_gaps\tncbi_species_taxid\tncbi_ssu_count\tncbi_strain_identifiers\tncbi_submitter\tncbi_taxid\tncbi_taxonomy\tncbi_taxonomy_unfiltered\tncbi_total_gap_length\tncbi_total_length\tncbi_translation_table\tncbi_trna_count\tncbi_type_material_designation\tncbi_ungapped_length\tncbi_unspanned_gaps\tncbi_wgs_master\tprotein_count\tscaffold_count\tssu_contig_len\tssu_count\tssu_gg_blast_align_len\tssu_gg_blast_bitscore\tssu_gg_blast_evalue\tssu_gg_blast_perc_identity\tssu_gg_blast_subject_id\tssu_gg_taxonomy\tssu_length\tssu_query_id\tssu_silva_blast_align_len\tssu_silva_blast_bitscore\tssu_silva_blast_evalue\tssu_silva_blast_perc_identity\tssu_silva_blast_subject_id\tssu_silva_taxonomy\ttotal_gap_length\ttrna_aa_count\ttrna_count\ttrna_selenocysteine_count\n+RS_GCF_000381545.1\t0\t100\t0\t439\to__Cytophagales (UID2938)\t266\t0\t4504205\t86.72438016743745\t62\t2169018\t41.82850570687274\t5193701\tRS_GCF_000381545.1\tt\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum;s__Rhodonellum psychrophilum\ttype strain of species\tLPSN\tt\t8\t7\t627008\t627008\t2894\t1\t2836\tNZ_KB906716.1\t113481\t2\t98\tNZ_KB906690.1\t2836\t5238\t0\t100\tFNQC01000038.312.3153\tBacteria;Bacteroidota;Bacteroidia;Cytophagales;Cyclobacteriaceae;Rhodonellum;Rhodonellum ikkaensis\t83637\t101837\tt\tf\tf\t194487\t212581\tScaffold\tASM38154v1\tna\tPRJNA224116\tSAMN02441658\t62\t194487\tnone\t2013-04-24\tGCA_000381545.1\tnone\tfull\tnone\tnone\t61.18350 N 48.01654 W\t0\t0\tRhodonellum psychrophilum GCM71 = DSM 17998\t4375\tna\t5\t51\t7\t212581\t128523\t70373\t2013/04/24\t11\t336828\t2\tDSM 17998\tDOE Joint Genome Institute\t1123057\td__Bacteria;p__Bacteroidetes;c__Cytophagia;o__Cytophagales;f__Cytophagaceae;g__Rhodonellum;s__Rhodonellum psychrophilum\td__Bacteria;x__FCB group;x__Bacteroidetes/Chlorobi group;p__Bacteroidetes;c__Cytophagia;o__Cytophagales;f__Cytophagaceae;g__Rhodonellum;s__Rhodonellum psychrophilum;x__Rhodonellum psychrophilum GCM71 = DSM 17998\t8199\t5193701\t11\t37\tassembly from type material\t5185502\t0\tARMB00000000.1\t4430\t51\t1472\t2\t1328\t2440\t0\t99.849\t130535\tk__Bacteria;p__Bacteroidetes;c__Cytophagia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum;s__psychrophilum\t1419\tNZ_KB906721.1\t1396\t2523\t0\t99.284\tHM127463.1.1447\tBacteria;Bacteroidota;Bacteroidia;Cytophagales;Cyclobacteriaceae;uncultured bacterium\t8199\t19\t37\t0\n+RS_GCF_000507905.1\t0\t99.29\t0.36\t530\tg__Prevotella (UID2721)\t280\t0\t2630658\t87.97710625711917\t14\t1333473\t44.71797427331401\t2990162\tRS_GCF_000185145.2\tf\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella oralis\tnot type material\tnone\tf\t2\t2\t948221\t1135470\t1135470\t3\t2939\tNZ_KI669541'..b'14\t19\t0\n+GB_GCA_002373285.1\t0\t98.8\t0.49\t487\to__Bacteroidales (UID2716)\t270\t0\t3342933\t90.31746563517713\t25\t1833032\t49.5290632982808\t3701314\tGB_GCA_900314655.1\tf\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900314655\tnot type material\tnone\tf\t7\t6\t340025\t397649\t297941\t1\t300\tDFKF01000002.1\t297941\t4\t109\tDFKF01000002.1\t301\t427\t3.18e-118\t92.359\tFNUV01000014.1.2381\tBacteria;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella ruminicola\t148036\t185065\tf\tf\tt\t203313\t283256\tScaffold\tASM237328v1\tna\tPRJNA348753\tSAMN06453981\t25\t203313\tnone\t2017-09-26\tGCA_002373285.1\tderived from metagenome\tfull\tUBA3652\tlow methane producing sheep\tnone\t0\tnone\tPrevotella sp. UBA3652\t0\tna\tnone\t20\t6\t283256\t249422\t95781\t2017/09/26\t5\t1947138\tnone\tUBA3652\tUniversity of Queensland\t1947138\td__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__\td__Bacteria;x__FCB group;x__Bacteroidetes/Chlorobi group;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;x__unclassified Prevotella;s__Prevotella sp. UBA3652\t392\t3701314\tnone\tnone\tnone\t3700922\t0\tDFKF00000000.1\t3064\t20\t167963\t1\tnone\tnone\tnone\tnone\tnone\tnone\t240\tDFKF01000013.1\t236\t340\t3.73e-92\t92.797\tFJ172841.1.1487\tBacteria;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;uncultured bacterium\t392\t19\t46\t0\n+GB_GCA_002313435.1\t16\t84.08\t2.3\t316\tp__Bacteroidetes (UID2605)\t210\t33.33\t2539257\t89.01019394826994\t407\t1447093\t50.930109867523356\t2852771\tGB_GCA_002314195.1\tf\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides;s__Cryptobacteroides sp002314195\tnot type material\tnone\tf\t78\t55\t35093\t78440\t25328\t1\t1036\tDCBI01000141.1\tnone\t0\tnone\tnone\t539\t809\t0\t93.878\tCDYK01020309.1522.4386\tBacteria;Bacteroidota;Bacteroidia;Bacteroidales;Rikenellaceae;Rikenellaceae RC9 gut group;gut metagenome\t6981\t12512\tf\tf\tt\t12489\t16866\tScaffold\tASM231343v1\tna\tPRJNA348753\tSAMN06454814\t407\t12489\tKenya\t2017-09-20\tGCA_002313435.1\tderived from metagenome\tfull\tUBA1111\tfeces\tnone\t0\tnone\tBacteroidales bacterium UBA1111\t0\tna\tnone\t228\t55\t16866\t10520\t5851\t2017/09/20\t179\t1950376\tnone\tUBA1111\tUniversity of Queensland\t1950376\td__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__\td__Bacteria;x__FCB group;x__Bacteroidetes/Chlorobi group;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;x__unclassified Bacteroidales;s__Bacteroidales bacterium UBA1111\t11424\t2852771\tnone\tnone\tnone\t2841347\t0\tDCBI00000000.1\t2394\t228\tnone\t0\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\tnone\t11424\t14\t23\t0\n+GB_GCA_002344345.1\t183\t96.66\t0.25\t302\tp__Bacteroidetes (UID2591)\t202\t0\t3615675\t83.29783565122254\t231\t1697428\t39.12102449575527\t4340659\tGB_GCA_002344345.1\tt\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA2365;s__UBA2365 sp002344345\tnot type material\tnone\tf\t48\t46\t95773\t106491\t19765\t1\t1964\tDDTL01000034.1\tnone\t0\tnone\tnone\t1996\t2039\t0\t85.621\tAATN01000936.161.2994\tBacteria;Bacteroidota;Ignavibacteria;SJA-28;metagenome\t18783\t20969\tf\tf\tt\t29093\t31568\tScaffold\tASM234434v1\tna\tPRJNA348753\tSAMN06455966\t231\t29093\tAustralia: Brisbane; Thorneside Wastewater Treatment Plant\t2017-09-22\tGCA_002344345.1\tderived from metagenome\tfull\tUBA2365\tactivated sludge\tnone\t0\tnone\tSaprospiraceae bacterium UBA2365\t0\tna\tnone\t207\t46\t31568\t18246\t9750\t2017/09/22\t24\t1952870\tnone\tUBA2365\tUniversity of Queensland\t1952870\td__Bacteria;p__Bacteroidetes;c__Saprospiria;o__Saprospirales;f__Saprospiraceae;g__;s__\td__Bacteria;x__FCB group;x__Bacteroidetes/Chlorobi group;p__Bacteroidetes;c__Saprospiria;o__Saprospirales;f__Saprospiraceae;x__unclassified Saprospiraceae;s__Saprospiraceae bacterium UBA2365\t1561\t4340659\tnone\tnone\tnone\t4339098\t0\tDDTL00000000.1\t3382\t207\t19765\t1\tnone\tnone\tnone\tnone\tnone\tnone\t1525\tDDTL01000034.1\t1493\t2612\t0\t98.326\tFJ716291.1.1496\tBacteria;Bacteroidota;Bacteroidia;Chitinophagales;Saprospiraceae;uncultured;uncultured bacterium\t1561\t19\t34\t0\n' |
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| diff -r 000000000000 -r ab933d3c6057 tool-data/gtdbtk_database_metadata_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gtdbtk_database_metadata_versioned.loc.sample Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,2 @@ +#value name version path +#test-gtdb Test bac 214 test-db \ No newline at end of file |
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| diff -r 000000000000 -r ab933d3c6057 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="gtdbtk_database_metadata_versioned" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="tool-data/gtdbtk_database_metadata_versioned.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r ab933d3c6057 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Aug 25 14:55:35 2024 +0000 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="gtdbtk_database_metadata_versioned" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="${__HERE__}/test-data/gtdbtk_database_metadata_versioned.loc.test" /> + </table> +</tables> |