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Changeset 0:6edfb4b6db85 (2025-01-16)

Next changeset 1:9e8cf8dd6955 (2025-02-10)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr commit 45daaecba3332d984a900727bf348ffb07a07154

added:
staramr_search.xml
test-data/16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa
test-data/16S-rc_gyrA-rc_beta-lactam.fsa
test-data/genes_to_exclude.tsv
test-data/staramr_database.loc
test-data/test-aminoglycoside.fsa
tool-data/staramr_database.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

diff -r 000000000000 -r 6edfb4b6db85 staramr_search.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/staramr_search.xml Thu Jan 16 08:29:08 2025 +0000

[

b'@@ -0,0 +1,1036 @@\n+<tool id="staramr_search" name="staramr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">0.11.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">22.05</token>\n+ <xml name="element_assert" token_name="" token_text="">\n+ <element name="@NAME@">\n+ <assert_contents>\n+ <has_text text="@TEXT@"/>\n+ <yield/>\n+ </assert_contents>\n+ </element>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">staramr</requirement>\n+ \n+ <requirement type="package" version="2.23.0">mlst</requirement>\n+ </requirements>\n+ <version_command>staramr --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+#import re\n+#set ext = \'.fasta\'\n+#set $named_genomes = \'\'\n+#for $genome in $genomes\n+ #set $_named_genome = re.sub(r\'(\\s|\$|\$|\\/)\', \'_\', str($genome.element_identifier)) + $ext\n+ ln -s \'$genome\' $_named_genome &&\n+ #set $named_genomes = $named_genomes + \' \' + $_named_genome\n+#end for\n+\n+\n+##Used only for test \n+#if str($hide_db_build) == \'true\':\n+staramr db build \n+ --dir resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502\n+ --resfinder-commit d1e607b\n+ --pointfinder-commit 694919f\n+ --plasmidfinder-commit 3e77502 &&\n+#end if\n+##\n+\n+staramr search\n+\n+ -d \'$staramr_db_select.fields.path\'\n+ --nprocs "\\${GALAXY_SLOTS:-1}"\n+\n+ --genome-size-lower-bound $advanced.genome_size_lower_bound\n+ --genome-size-upper-bound $advanced.genome_size_upper_bound\n+ --minimum-N50-value $advanced.minimum_N50_value\n+ --minimum-contig-length $advanced.minimum_contig_length\n+ --unacceptable-number-contigs $advanced.unacceptable_number_contigs\n+\n+ --pid-threshold $advanced.pid_threshold\n+ --percent-length-overlap-resfinder $advanced.percent_length_overlap_resfinder\n+ --percent-length-overlap-plasmidfinder $advanced.percent_length_overlap_plasmidfinder\n+ --percent-length-overlap-pointfinder $advanced.percent_length_overlap_pointfinder\n+\n+#if str($advanced.mlst_scheme) != \'auto\':\n+ --mlst-scheme \'${advanced.mlst_scheme}\'\n+#end if\n+\n+$advanced.report_all_blast\n+$advanced.exclude_negatives\n+$advanced.exclude_resistance_phenotypes\n+\n+#if str($advanced.exclude_genes.exclude_genes_condition) == \'custom\'\n+ --exclude-genes-file \'${advanced.exclude_genes.exclude_genes_file}\'\n+#elif str($advanced.exclude_genes.exclude_genes_condition) == \'none\'\n+ --no-exclude-genes\n+#end if\n+\n+#if $advanced.complex_mutations_file\n+ --complex-mutations-file \'$advanced.complex_mutations_file\'\n+#end if\n+\n+#if str($advanced.plasmidfinder_type) != \'include_all\'\n+ --plasmidfinder-database-type \'${advanced.plasmidfinder_type}\'\n+#end if\n+\n+ --output-summary \'$summary\'\n+ --output-detailed-summary \'$detailed_summary\'\n+ --output-resfinder \'$resfinder\'\n+ --output-plasmidfinder \'$plasmidfinder\'\n+ --output-settings \'$settings\'\n+ --output-excel results.xlsx\n+ --output-mlst \'$mlst\'\n+\n+ --output-hits-dir staramr_hits\n+\n+#if str($pointfinder_organism) != \'disabled\'\n+ --output-pointfinder \'$pointfinder\'\n+ --pointfinder-organism \'${pointfinder_organism}\'\n+#end if\n+\n+$named_genomes &&\n+#if str($hide_db_build) == \'true\':\n+ rm -r resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <param name="hide_db_build" type="hidden" value="" />\n+ <param type="data" name="genom'..b' contig00008 | 22801 | 20165 | S83Y | | | Target modification | 7492118,10471553 |\n+| 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 |\n++------------+-------------+-----------------------------------+------------------------------+-------+----------+---------------------+-----------+----------+-------------------------+-------------+--------+--------+----------------------+-----------+-----------------------+---------------------+------------------+\n+\n+\n+settings.txt\n+````````````\n+\n+The command-line, database versions, and other settings used to run `staramr`.\n+\n+::\n+\n+ command_line = staramr search --pointfinder-organism enterococcus_faecium -o out pbp5.fa\n+ version = 0.10.0\n+ start_time = 2023-08-23 13:37:41\n+ end_time = 2023-08-23 13:37:42\n+ total_minutes = 0.02\n+ resfinder_db_dir = staramr/databases/data/dist/resfinder\n+ resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git\n+ resfinder_db_commit = fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd\n+ resfinder_db_date = Tue, 24 May 2022 06:51\n+ pointfinder_db_dir = staramr/databases/data/dist/pointfinder\n+ pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git\n+ pointfinder_db_commit = 8c694b9f336153e6d618b897b3b4930961521eb8\n+ pointfinder_db_date = Mon, 01 Feb 2021 15:46\n+ pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus\n+ pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella\n+ plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder\n+ plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git\n+ plasmidfinder_db_commit = c18e08c17a5988d4f075fc1171636e47546a323d\n+ plasmidfinder_db_date = Wed, 18 Jan 2023 09:45\n+ mlst_version = 2.23.0\n+ pointfinder_organism = enterococcus_faecium\n+ pointfinder_gene_drug_version = 072621.2\n+ resfinder_gene_drug_version = 072621\n+\n+results.xlsx\n+````````````\n+\n+An Excel spreadsheet containing the previous 5 files as separate worksheets.\n+\n+BLAST Hits\n+``````````\n+\n+The dataset collection **hits** stores fasta files of the specific blast hits.\n+\n+.. _staramr: https://github.com/phac-nml/staramr\n+.. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db\n+.. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db\n+.. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db\n+.. _webservices: http://www.genomicepidemiology.org/services/\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.3390/microorganisms1002029</citation>\n+ </citations>\n+ <creator>\n+ <person givenName="Aaron" familyName="Petkau" identifier="apetkau" email="aaron.petkau@gmail.com"/>\n+ <person givenName="Jennifer" familyName="Tran" identifier="jennifertran" email="jennifer.tran101@gmail.com"/>\n+ <person givenName="Saskia" familyName="Hiltemann" identifier="shiltemann" email="saskia.hiltemann@gmail.com"/>\n+ <person givenName="Helena" familyName="Rasche" identifier="hexylena" email="hexylena@galaxians.org"/>\n+ <person givenName="Eric" familyName="Marinier" identifier="emarinier"/>\n+ </creator>\n+</tool>\n'

diff -r 000000000000 -r 6edfb4b6db85 test-data/16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa Thu Jan 16 08:29:08 2025 +0000

@@ -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 -r 000000000000 -r 6edfb4b6db85 test-data/16S-rc_gyrA-rc_beta-lactam.fsa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/16S-rc_gyrA-rc_beta-lactam.fsa Thu Jan 16 08:29:08 2025 +0000

diff -r 000000000000 -r 6edfb4b6db85 test-data/genes_to_exclude.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes_to_exclude.tsv Thu Jan 16 08:29:08 2025 +0000

@@ -0,0 +1,2 @@
+gene_id
+aac(6')-Iaa_1_NC_003197

diff -r 000000000000 -r 6edfb4b6db85 test-data/staramr_database.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/staramr_database.loc Thu Jan 16 08:29:08 2025 +0000

@@ -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 -r 000000000000 -r 6edfb4b6db85 test-data/test-aminoglycoside.fsa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-aminoglycoside.fsa Thu Jan 16 08:29:08 2025 +0000

@@ -0,0 +1,9 @@
+>aac(6')-Iaa_1_NC_003197
+ATGGACATCAGGCAAATGAACAGAACCCATCTGGATCACTGGCGCGGATTGCGAAAACAG
+CTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCC
+GATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCC
+TCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGT
+ATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTG
+CAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAAT
+ACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTC
+TACCGAAAGCGTTGTTGA

diff -r 000000000000 -r 6edfb4b6db85 tool-data/staramr_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/staramr_database.loc.sample Thu Jan 16 08:29:08 2025 +0000

@@ -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 -r 000000000000 -r 6edfb4b6db85 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Jan 16 08:29:08 2025 +0000

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="staramr_database" comment_char="#">
+        <columns>value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit</columns>
+        <file path="tool-data/staramr_database.loc.sample"/>
+    </table>
+</tables>
\ No newline at end of file

diff -r 000000000000 -r 6edfb4b6db85 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Jan 16 08:29:08 2025 +0000

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="staramr_database" comment_char="#">
+        <columns>value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit</columns>
+        <file path="${__HERE__}/test-data/staramr_database.loc"/>
+    </table>
+</tables>
\ No newline at end of file