diff --git a/data_managers/data_manager_build_staramr/.shed.yml b/data_managers/data_manager_build_staramr/.shed.yml new file mode 100644 index 00000000000..7f7e7d59ede --- /dev/null +++ b/data_managers/data_manager_build_staramr/.shed.yml @@ -0,0 +1,10 @@ +name: data_manager_build_staramr +owner: iuc +description: "Download the Resfinder, Pointfinder and Plasmidfinder databases for staramr search command" +homepage_url: "https://github.com/phac-nml/staramr" +long_description: | + Download the Resfinder, Pointfinder and Plasmidfinder databases for starAMR using the commits corresponding to the versions of the different databases. +remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_staramr" +type: unrestricted +categories: +- Data Managers \ No newline at end of file diff --git a/data_managers/data_manager_build_staramr/data_manager/data_manager_build_staramr_download.xml b/data_managers/data_manager_build_staramr/data_manager/data_manager_build_staramr_download.xml new file mode 100644 index 00000000000..c8d8cad1bd0 --- /dev/null +++ b/data_managers/data_manager_build_staramr/data_manager/data_manager_build_staramr_download.xml @@ -0,0 +1,117 @@ + + + + 0.10.0 + 0 + 22.05 + + + + + + + + + + + staramr + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.3390/microorganisms10020292 + + \ No newline at end of file diff --git a/data_managers/data_manager_build_staramr/data_manager_conf.xml b/data_managers/data_manager_build_staramr/data_manager_conf.xml new file mode 100644 index 00000000000..c6681ca2795 --- /dev/null +++ b/data_managers/data_manager_build_staramr/data_manager_conf.xml @@ -0,0 +1,22 @@ + + + + + + + + + + ${path} + staramr/${path} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/staramr/${path} + abspath + + + + + + + + diff --git a/data_managers/data_manager_build_staramr/test-data/staramr_database.loc.test b/data_managers/data_manager_build_staramr/test-data/staramr_database.loc.test new file mode 100644 index 00000000000..65e7509a92f --- /dev/null +++ b/data_managers/data_manager_build_staramr/test-data/staramr_database.loc.test @@ -0,0 +1,11 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path resfinder_commit pointfinder_commit plasmidfinder_commit +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data d1e607b 694919f 3e77502 +staramr_downloaded_13012025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 starAMR databases with ResFinder: 2.4.0_d1e607b_2024-08-06, PointFinder: 4.1.1_694919f_2024-08-08, PlasmidFinder: 3e77502_2024-03-07 /tmp/tmpc6qeamum/galaxy-dev/tool-data/staramr/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 d1e607b 694919f 3e77502 \ No newline at end of file diff --git a/data_managers/data_manager_build_staramr/tool-data/staramr_database.loc.sample b/data_managers/data_manager_build_staramr/tool-data/staramr_database.loc.sample new file mode 100644 index 00000000000..f27dc5a309c --- /dev/null +++ b/data_managers/data_manager_build_staramr/tool-data/staramr_database.loc.sample @@ -0,0 +1,10 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path resfinder_commit pointfinder_commit plasmidfinder_commit +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data d1e607b 694919f 3e77502 \ No newline at end of file diff --git a/data_managers/data_manager_build_staramr/tool_data_table_conf.xml.sample b/data_managers/data_manager_build_staramr/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..93a3e0bd6c2 --- /dev/null +++ b/data_managers/data_manager_build_staramr/tool_data_table_conf.xml.sample @@ -0,0 +1,6 @@ + + + value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit + +
+ \ No newline at end of file diff --git a/data_managers/data_manager_build_staramr/tool_data_table_conf.xml.test b/data_managers/data_manager_build_staramr/tool_data_table_conf.xml.test new file mode 100644 index 00000000000..a188366464e --- /dev/null +++ b/data_managers/data_manager_build_staramr/tool_data_table_conf.xml.test @@ -0,0 +1,6 @@ + + + value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit + +
+ \ No newline at end of file diff --git a/tools/staramr/.shed.yml b/tools/staramr/.shed.yml new file mode 100644 index 00000000000..a3ad768a3d5 --- /dev/null +++ b/tools/staramr/.shed.yml @@ -0,0 +1,7 @@ +categories: [Sequence Analysis] +description: Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. +name: staramr +owner: iuc +long_description: staramr - Scans genome contigs (in FASTA format) against the ResFinder, PlasmidFinder, and PointFinder databases to search for antimicrobial resistance genomes. Makes predictions of the drugs these genes give resistance to. +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr +homepage_url: https://github.com/phac-nml/staramr diff --git a/tools/staramr/staramr_search.xml b/tools/staramr/staramr_search.xml new file mode 100644 index 00000000000..5e7fd376a1c --- /dev/null +++ b/tools/staramr/staramr_search.xml @@ -0,0 +1,1036 @@ + + Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes + + 0.11.0 + 0 + 22.05 + + + + + + + + + + + staramr + + mlst + + staramr --version + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + output_files['output_selection'] and "mlst_table" in output_files['output_selection'] + + + output_files['output_selection'] and "summary_table" in output_files['output_selection'] + + + output_files['output_selection'] and "detailed_summary_table" in output_files['output_selection'] + + + output_files['output_selection'] and "resfinder_table" in output_files['output_selection'] + + + output_files['output_selection'] and "plasmidfinder_table" in output_files['output_selection'] + + + pointfinder_organism != "disabled" + output_files['output_selection'] and "pointfinder_table" in output_files['output_selection'] + + + output_files['output_selection'] and "settings_output" in output_files['output_selection'] + + + output_files['output_selection'] and "excel_output" in output_files['output_selection'] + + + + + + + + + + + +
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+ + + + + + + + TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 | S83Y | | | Target modification | 7492118,10471553 | +| SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | Nalidixic acid,Ciprofloxacin | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 | S83Y | | | Target modification | 7492118,10471553 | ++------------+-------------+-----------------------------------+------------------------------+-------+----------+---------------------+-----------+----------+-------------------------+-------------+--------+--------+----------------------+-----------+-----------------------+---------------------+------------------+ + + +settings.txt +```````````` + +The command-line, database versions, and other settings used to run `staramr`. + +:: + + command_line = staramr search --pointfinder-organism enterococcus_faecium -o out pbp5.fa + version = 0.10.0 + start_time = 2023-08-23 13:37:41 + end_time = 2023-08-23 13:37:42 + total_minutes = 0.02 + resfinder_db_dir = staramr/databases/data/dist/resfinder + resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git + resfinder_db_commit = fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd + resfinder_db_date = Tue, 24 May 2022 06:51 + pointfinder_db_dir = staramr/databases/data/dist/pointfinder + pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git + pointfinder_db_commit = 8c694b9f336153e6d618b897b3b4930961521eb8 + pointfinder_db_date = Mon, 01 Feb 2021 15:46 + pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus + pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella + plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder + plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git + plasmidfinder_db_commit = c18e08c17a5988d4f075fc1171636e47546a323d + plasmidfinder_db_date = Wed, 18 Jan 2023 09:45 + mlst_version = 2.23.0 + pointfinder_organism = enterococcus_faecium + pointfinder_gene_drug_version = 072621.2 + resfinder_gene_drug_version = 072621 + +results.xlsx +```````````` + +An Excel spreadsheet containing the previous 5 files as separate worksheets. + +BLAST Hits +`````````` + +The dataset collection **hits** stores fasta files of the specific blast hits. + +.. _staramr: https://github.com/phac-nml/staramr +.. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db +.. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db +.. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db +.. _webservices: http://www.genomicepidemiology.org/services/ + ]]> + + 10.3390/microorganisms1002029 + + + + + + + + + diff --git a/tools/staramr/test-data/16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa b/tools/staramr/test-data/16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa new file mode 120000 index 00000000000..a5aa69c26d6 --- /dev/null +++ b/tools/staramr/test-data/16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa @@ -0,0 +1 @@ +16S-rc_gyrA-rc_beta-lactam.fsa \ No newline at end of file diff --git a/tools/staramr/test-data/16S-rc_gyrA-rc_beta-lactam.fsa b/tools/staramr/test-data/16S-rc_gyrA-rc_beta-lactam.fsa new file mode 100644 index 00000000000..c86a07c7748 --- /dev/null +++ b/tools/staramr/test-data/16S-rc_gyrA-rc_beta-lactam.fsa @@ -0,0 +1,88 @@ +>16S_rrsD rc (C1065T), gyrA rc G199C A67P, blaIMP-42_1_AB753456 +gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg +AGGTAAGGAGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCC +AGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGC +AACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGG +CATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAAT +CCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTAT +GCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCC +CCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGACCTAATCGCTGGCA +ACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTa +ACGACAGCCATGCAGCACCTGTCTCACAGTTCCCGAAGGCACCAATCCATCTCTGGAAAG +TTCTGTGGATGTCAAGACCAGGTAAGGTTCTTCGCGTTGCATCGAATTAAACCACATGCT +CCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTTTTAACCTTGCGGCCGTACTCCC +CAGGCGGTCTACTTAACGCGTTAGCTCCGGAAGCCACGCCTCAAGGGCACAACCTCCAAG +TAGACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTT +CGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGAT +CTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGC +CAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCG +CCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCG +GCTGCTGGCACGGAGTTAGCCGGTGCTTCTTCTGCGGGTAACGTCAATTGCTGCGGTTAT +TAACCACAACACCTTCCTCCCCGCTGAAAGTACTTTACAACCCGAAGGCCTTCTTCATAC +ACGCGGCATGGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCC +GTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAG +GGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACAAGCTAATCCCATCTGGGCACATCT +GATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCCA +CCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGTTTCCCAGACATTACTCACCCGTCCG +CCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGACTTGCATGTGTTAGGC +CTGCCGCCAGCGTTCAATCTGAGCCATGATCAAACTCTTCAATTgggggggggggggggg +gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg +TTACTCGTCAGCGTCATCCGCAACGTCGTCATCGCTTTCCGCTTCCGGGGCGATATCCTC +ATCCCCTTCCGCCACGCTGCCGTCGATAGCGTCGAGTTCTTCGTCATCTACCGGTTCAGC +AACGCGTTGCAGACCCACCACGTTTTCATCTTCCGCCGTGCGGATAAGGATAACGCCCTG +GGTATTACGTCCCACGACGCTGATCTCGGACACTCGGGTACGCACCAGAGTACCGGCATC +CGTGATCATCATGATCTGGTCGCAATCGTCTACCTGTACCGCACCGACAACGGAACCGTT +GCGCTCGGTCACTTTGATAGAGATAACGCCCTGCGTCGCACGAGACTTGGTCGGGTACTC +GTCCGCTGCGGTACGCTTCCCGTAGCCGTTTTGCGTTACGGTCAGAATAGCGCCTTCGCC +GCGTGGGATGATCAGAGAGACGACTTTATCGTCTCCCGCCAGCTTAATACCGCGCACACC +GGTCGCGGTACGCCCCATCGCACGGACGGCGTCTTCTTTGAAGCGCACCACTTTACCCGC +GGCCGAGAACAGCATGACTTCGTCAGAACCAGAAGTCAGGTCAACGCCAATCAGCTCGTC +GCCGTCGTTGAGGTTCACCGCGATAATACCGGCGGAACGCGGACGGCTGAATTCGGTCAG +CGCCGTTTTCTTCACGGTACCGCTGGCGGTCGCCATAAAGACGTTGACGCCTTCTTCGTA +TTCACGAACCGGCAGAATCGCGGTGATACGTTCGTTGGCTTCCAGCGGCAGCAGGTTAAC +GATCGGACGACCGCGCGCGCCGCGGCTGGCTTCCGGCAACTGATAGACCTTCATCCAGTA +CAGACGGCCCCGGCTGGAGAAGCAGAGGATGGTGTCATGGGTGTTGGCCACCAGCAGGCG +GTCGATAAAGTCTTCTTCTTTAATACGCGCGGCAGATTTACCTTTCCCACCACGACGTTG +CGCTTCGTAATCCGTCAGCGGTTGATATTTGACGTAACCCTGGTGAGACAGCGTCACGAC +AACATCTTCCTGGCTAATCAGATCTTCGATATTAATATCGGCGCTGTTGGCGGTGATTTC +GGTACGACGCTCATCGCCGAACTGATCGCGAATTAACTCCATCTCTTCGCGGATCACTTC +CATCAGGCGATCGGCGCTGCCCAGAATGTGCAGCAGTTCAGCAATCTGCTCCAGCAACTC +TTTGTATTCGTCGAGCAGTTTTTCATGCTCCAGGCCGGTCAGTTTCTGCAAACGCAGATC +CAGAATCGCCTGCGCCTGCTGCTCAGTCAGGTAATACTGACCGTCACGCACGCCAAATTC +TGGCTCCAGCCATTCCGGACGCGCAGCGTCATCACCAGCGCGCTCCAGCATCGCAGCAAC +GTTGCCCAGATCCCACGGACGCGAAATCAGCGCCGCTTTTGCTTCTGCCGGCGTTGGCGC +GCGGCGAATCAGTTCGATAATCGGGTCGATGTTAGCCAGCGCAATCGCCAGAGCTTCAAG +GATATGCGCGCGGTCACGGGCTTTACGCAGTTCAAAAATAGTACGACGCGTCACCACTTC +ACGGCGGTGGCGCACGAACGCTGAAATGATGTCTTTCAGGTTCATGATCTTCGGCTGGCC +GTGATGCAGCGCCACCATGTTAATACCGAAGGAAACCTGTAGCTGGGTCTGGGAGTAGAG +ATTATTAAGCACCACCTCGCCCACCGCATCGCGTTTCACTTCAATCACGATGCGCATCCC +GTCTTTGTCGGATTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTATCTTTCACCAG +CTCGGCGATTTTCTCGATCAGGCGCGCTTTGTTCACCTGATAGGGAATTTCATGGACGAT +GATGGTTTCACGGCCCGTTTTCGCGTCAGCTTCAACTTCCGCGCGGGCGCGAATGTACAC +TTTGCCACGACCGGTACGGTAGGCTTCTTCGATACCACGACGACCGTTGATGATCGCGGC +GGTCGGGAAGTCCGGCCCCGGAATATGTTCCATCAGCCCTTCAATGCTGATGTCTTCGTT +GTCGATATACGCCAGGCAGCCGTTAATCACTTCCGTCAGGTTGTGCGGCGGGATATTCGT +CGCCATACCTACTGCGATACCGGAAGAACCGTTCACCAGCAGATTCGGAATTTTGGTCGG +CATGACGTCCGGAATTTTTTCCGTACCGTCATAGTTATCCACGAAATCCACCGTCTCTTT +TTCGAGATCGGCCATCAGTTCGTGGGCGATTTTCGCCAGACGGATCTCCGTATAACGCAT +TGCCGCCGCGGAGTCGCCGTCAATAGAACCGAAGTTACCCTGACCATCCACCAGCATGTA +ACGCAGCGAGAATGGCTGCGCCATACGAACGATGGTGTCATACACTGCGGAATCGCCGTG +GGGATGGTATTTACCGATTACGTCACCAACGACACGGGgAGATTTTTTATAGGCTTTGTT +CCAGTCATTGCCCAATACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCC +ATCTCGGACATCCGGCAGCGCACGGCCAACAATGACCGACATCGCATAATCCAGATAGGA +GCTTTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATggg +gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg +ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAG +TCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTT +GAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCT +GAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGG +TTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGC +ACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACA +AATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAAC +TATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGAT +AACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCG +TACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTA +TTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGAC +GCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAA +CCATCAAAACCAAGCAACTAAggggggggggggggggggggggggggggggggggggggg +gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg diff --git a/tools/staramr/test-data/genes_to_exclude.tsv b/tools/staramr/test-data/genes_to_exclude.tsv new file mode 100644 index 00000000000..47ab30a0428 --- /dev/null +++ b/tools/staramr/test-data/genes_to_exclude.tsv @@ -0,0 +1,2 @@ +gene_id +aac(6')-Iaa_1_NC_003197 diff --git a/tools/staramr/test-data/staramr_database.loc b/tools/staramr/test-data/staramr_database.loc new file mode 100644 index 00000000000..b69021ec1a9 --- /dev/null +++ b/tools/staramr/test-data/staramr_database.loc @@ -0,0 +1,11 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path resfinder_commit pointfinder_commit plasmidfinder_commit +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data d1e607b 694919f 3e77502 +staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 starAMR databases with ResFinder: 2.4.0_d1e607b_2024-08-06, PointFinder: 4.1.1_694919f_2024-08-08, PlasmidFinder: 3e77502_2024-03-07 resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 d1e607b 694919f 3e77502 \ No newline at end of file diff --git a/tools/staramr/test-data/test-aminoglycoside.fsa b/tools/staramr/test-data/test-aminoglycoside.fsa new file mode 100644 index 00000000000..cce653aa23e --- /dev/null +++ b/tools/staramr/test-data/test-aminoglycoside.fsa @@ -0,0 +1,9 @@ +>aac(6')-Iaa_1_NC_003197 +ATGGACATCAGGCAAATGAACAGAACCCATCTGGATCACTGGCGCGGATTGCGAAAACAG +CTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCC +GATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCC +TCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGT +ATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTG +CAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAAT +ACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTC +TACCGAAAGCGTTGTTGA diff --git a/tools/staramr/tool-data/staramr_database.loc.sample b/tools/staramr/tool-data/staramr_database.loc.sample new file mode 100644 index 00000000000..1d3296545d3 --- /dev/null +++ b/tools/staramr/tool-data/staramr_database.loc.sample @@ -0,0 +1,3 @@ +#This is a sample file distributed with Galaxy that enables tools +#file has this format (white space characters are TAB characters) +#V4.0_2022-08-29 7025248 1.5 path/to/db \ No newline at end of file diff --git a/tools/staramr/tool_data_table_conf.xml.sample b/tools/staramr/tool_data_table_conf.xml.sample new file mode 100644 index 00000000000..6e4275f42cf --- /dev/null +++ b/tools/staramr/tool_data_table_conf.xml.sample @@ -0,0 +1,7 @@ + + + + value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit + +
+ \ No newline at end of file diff --git a/tools/staramr/tool_data_table_conf.xml.test b/tools/staramr/tool_data_table_conf.xml.test new file mode 100644 index 00000000000..f8d47a5b8d8 --- /dev/null +++ b/tools/staramr/tool_data_table_conf.xml.test @@ -0,0 +1,7 @@ + + + + value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit + +
+ \ No newline at end of file