| Previous changeset 17:141afacabcfa (2023-08-31) Next changeset 19:3548a93b39c1 (2024-12-18) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed |
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modified:
staramr_search.xml |
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| diff -r 141afacabcfa -r 3b22de20bd4b staramr_search.xml --- a/staramr_search.xml Thu Aug 31 15:55:49 2023 +0000 +++ b/staramr_search.xml Tue Sep 19 18:41:35 2023 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">\n+<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1" profile="16.04">\n <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>\n <macros>\n <token name="@VERSION@">0.10.0</token>\n@@ -419,7 +419,7 @@\n -----\n \n 1. Select your genome contigs (in FASTA format).\n-2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).\n+2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning.\n 3. Run the tool.\n \n Input\n@@ -441,6 +441,18 @@\n aac(6\')-Iaa_1_NC_003197\n ColpVC_1__JX133088\n \n+Complex mutations file\n+``````````````````````\n+\n+Complex mutations describe multiple point mutations that must be simultaneously present in order to confer resistance. Complex mutations may be specified by the user using a TSV-formatted file with the following format:\n+\n+::\n+\n+ positions mandatory phenotype\n+ mutation(s) mutation(s) phenotype\n+\n+Where "positions" are all the point mutations to group into the complex mutation (optional and mandatory), "mandatory" are all the point mutations that must be present for the complex mutation to be reported (mandatory is a subset of positions), and phenotype is the phenotype that is conferred when this set of mutations is present.\n+\n Output\n ------\n \n@@ -451,13 +463,13 @@\n \n A tabular file of each multi-locus sequence type (MLST) and it\'s corresponding locus/alleles, one genome per line.\n \n-+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+\n-| Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 |\n-+============+==============+===================================+============+============+============+============+============+============+============+\n-| SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |\n-+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+\n-| SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |\n-+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+\n++------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+\n+| Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 |\n++============+=====================+===============+=========+=========+=========+=========+=========+=========+==========+\n+| SRR1952908 | senterica_achtman_2 | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |\n+| SRR1952926 | senterica_achtman_2 | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |\n++------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+\n+\n \n \n summary.tsv\n@@ -465,13 +477,13 @@\n \n A summary of all detected AMR genes/mutations in each genome, one genome per line.\n \n-+------------+----------------+-----------------------------------------------------------+----'..b'8 | 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@@ -590,25 +547,29 @@\n \n ::\n \n- command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta\n- version = 0.7.1\n- start_time = 2019-04-25 16:01:32\n- end_time = 2019-04-25 16:01:34\n- total_minutes = 0.04\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 = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535\n- resfinder_db_date = Mon, 16 Jul 2018 16:58\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 = 8706a6363bb29e47e0e398c53043b037c24b99a7\n- pointfinder_db_date = Wed, 04 Jul 2018 14:27\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 = 81919954cbedaff39056610ab584ab4c06011ed8\n- plasmidfinder_db_date = Tue, 20 Nov 2018 08:51\n- pointfinder_gene_drug_version = 050218\n- resfinder_gene_drug_version = 050218.1\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@@ -620,7 +581,7 @@\n \n The dataset collection **hits** stores fasta files of the specific blast hits.\n \n-Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.\n+Galaxy wrapper written by Aaron Petkau and Eric Marinier at the National Microbiology Laboratory, Public Health Agency of Canada.\n \n .. _staramr: https://github.com/phac-nml/staramr\n .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db\n' |