# HG changeset patch
# User iuc
# Date 1737016148 0
# Node ID 6edfb4b6db852c3c92fa06d05a3aec0853bda538
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr commit 45daaecba3332d984a900727bf348ffb07a07154
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
@@ -0,0 +1,1036 @@
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+ Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes
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+ 0.11.0
+ 0
+ 22.05
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+ staramr
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+ mlst
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+ staramr --version
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+ output_files['output_selection'] and "mlst_table" in output_files['output_selection']
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+ output_files['output_selection'] and "summary_table" in output_files['output_selection']
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+ output_files['output_selection'] and "detailed_summary_table" in output_files['output_selection']
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+ output_files['output_selection'] and "resfinder_table" in output_files['output_selection']
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+ output_files['output_selection'] and "plasmidfinder_table" in output_files['output_selection']
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+ pointfinder_organism != "disabled"
+ output_files['output_selection'] and "pointfinder_table" in output_files['output_selection']
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+ output_files['output_selection'] and "settings_output" in output_files['output_selection']
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+ 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
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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
@@ -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/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 @@
+
+
+
+ value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit
+
+
+
\ 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 @@
+
+
+
+ value, name, path, resfinder_commit, pointfinder_commit, plasmidfinder_commit
+
+
+
\ No newline at end of file