staramr: staramr_search.xml comparison

comparison staramr_search.xml @ 18:3b22de20bd4b draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 1a2d7c4c5b7c0d3aac10d1d5fbd8d33550f840ed

author	nml
date	Tue, 19 Sep 2023 18:41:35 +0000
parents	141afacabcfa
children

comparison

equal deleted inserted replaced

-:141afacabcfa
+:3b22de20bd4b
-<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
+<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1" profile="16.04">
 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
 <macros>
 <token name="@VERSION@">0.10.0</token>
 </macros>
 <requirements>
 Usage
 -----
 1. Select your genome contigs (in FASTA format).
-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).
+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.
 3. Run the tool.
 Input
 -----
 #gene_id
 aac(6')-Iaa_1_NC_003197
 ColpVC_1__JX133088
+Complex mutations file
+``````````````````````
+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:
+::
+positions    mandatory    phenotype
+mutation(s)  mutation(s)  phenotype
+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.
 Output
 ------
 There are 6 different output files produced by `staramr` as well as a collection of additional files.
 mlst.tsv
 ````````````````````
 A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.
-+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
++------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+
-| Isolate ID | Scheme       | Sequence Type                     | Locus 1    | Locus 2    | Locus 3    | Locus 4    | Locus 5    | Locus 6    | Locus 7    |
+| Isolate ID | Scheme              | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7  |
-+============+==============+===================================+============+============+============+============+============+============+============+
++============+=====================+===============+=========+=========+=========+=========+=========+=========+==========+
-| SRR1952908 | senterica    | 11                                | aroC(5)    | dnaN(2)    | hemD(3)    | hisD(7)    | purE(6)    | sucA(6)    | thrA(11)   |
+| SRR1952908 | senterica_achtman_2 | 11            | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
-+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
+| SRR1952926 | senterica_achtman_2 | 11            | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) |
-| SRR1952926 | senterica    | 11                                | aroC(5)    | dnaN(2)    | hemD(3)    | hisD(7)    | purE(6)    | sucA(6)    | thrA(11)   |
++------------+---------------------+---------------+---------+---------+---------+---------+---------+---------+----------+
-+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
 summary.tsv
 ```````````
 A summary of all detected AMR genes/mutations in each genome, one genome per line.
-+------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
-| Isolate ID | Quality Module | Genotype                                                  | Predicted Phenotype                                                                                       | Plasmid                             | Scheme    | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback |
++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------+---------------------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
-+============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+
+| Isolate ID | Quality Module | Genotype                                                  | Predicted Phenotype                                                                                       | CGE Predicted Phenotype                                                                                                                                                                   | Plasmid                                      | Scheme              | Sequence Type | Genome Length | N50 value | Number of Contigs Greater Than Or Equal To 300 bp | Quality Module Feedback |
-| SRR1952908 | Passed         | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11            | 4796082       | 225419    | 59                                                |                         |
++============+================+===========================================================+===========================================================================================================+===========================================================================================================================================================================================+==============================================+=====================+===============+===============+===========+===================================================+=========================+
-+------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
+| SRR1952908 | Passed         | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | Spectinomycin, Streptomycin, Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin, Chloramphenicol, Nalidixic acid, Ciprofloxacin, Sulfamethoxazole, Doxycycline, Tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1-I(Alpha) | senterica_achtman_2 | 11            | 4785500       | 250423    | 41                                                |                         |
-| SRR1952926 | Passed         | blaTEM-57, gyrA (S83Y), tet(A)                            | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline                                               | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11            | 4794071       | 225380    | 50                                                |                         |
+| SRR1952926 | Passed         | blaTEM-57, gyrA (S83Y), tet(A)                            | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline                                               | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin, Nalidixic acid, Ciprofloxacin, Doxycycline, Tetracycline                                                                 | ColpVC, IncFIB(S), IncFII(S), IncI1-I(Alpha) | senterica_achtman_2 | 11            | 4785451       | 228311    | 40                                                |                         |
-+------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------+---------------------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
 detailed_summary.tsv
 ````````````````````
 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
++------------+----------------------------+------------+---------------------+-----------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+
-| Isolate ID | Gene/Plasmid | Predicted Phenotype               | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start  | End    | Accession | Data Type  |
+| Isolate ID | Data                       | Data Type  | Predicted Phenotype | CGE Predicted Phenotype     | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start | End  | Accession |
-+============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+
++============+============================+============+=====================+=============================+===========+==========+=========================+=============+=======+======+===========+
-| SRR1952908 | ColpVC       |                                   | 98.96     | 100      | 193/193                 | contig00038 | 1618   | 1426   | JX133088  | Plasmid    |
+| SRR1952908 | ST11 (senterica_achtman_2) | MLST       |                     |                             |           |          |                         |             |       |      |           |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
+| SRR1952908 | ColpVC                     | Plasmid    |                     |                             | 98.96     | 100.0    | 193/193                 | contig00038 | 1618  | 1426 | JX133088  |
-| SRR1952908 | IncFIB(S)    |                                   | 98.91     | 100      | 643/643                 | contig00024 | 10302  | 9660   | FN432031  | Plasmid    |
+| SRR1952908 | aadA1                      | Resistance | streptomycin        | Spectinomycin, Streptomycin | 100.0     | 100.0    | 792/792                 | contig00030 | 5355  | 4564 | JQ414041  |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
++------------+----------------------------+------------+---------------------+-----------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+
-| SRR1952908 | IncFII(S)    |                                   | 100       | 100      | 262/262                 | contig00024 | 54294  | 54555  | CP000858  | Plasmid    |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | IncI1        |                                   | 100       | 100      | 142/142                 | contig00020 | 3907   | 3766   | AP005147  | Plasmid    |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | aadA1        | streptomycin                      | 100       | 100      | 792/792                 | contig00030 | 5355   | 4564   | JQ414041  | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | aadA2        | streptomycin                      | 100       | 100      | 780/780                 | contig00030 | 7748   | 6969   | X68227    | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | blaTEM-57    | ampicillin                        | 99.88     | 100      | 861/861                 | contig00032 | 6247   | 5387   | FJ405211  | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | cmlA1        | chloramphenicol                   | 99.92     | 100      | 1260/1260               | contig00030 | 6707   | 5448   | M64556    | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid | 99.96     | 100      | 2637/2637               | contig00008 | 22801  | 20165  |           | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | sul3         | sulfisoxazole                     | 100       | 100      | 792/792                 | contig00030 | 2091   | 2882   | AJ459418  | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952908 | tet(A)       | tetracycline                      | 99.92     | 97.8     | 1247/1275               | contig00032 | 1476   | 2722   | AF534183  | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | ColpVC       |                                   | 98.96     | 100      | 193/193                 | contig00037 | 657    | 849    | JX133088  | Plasmid    |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | IncFIB(S)    |                                   | 98.91     | 100      | 643/643                 | contig00021 | 10302  | 9660   | FN432031  | Plasmid    |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | IncFII(S)    |                                   | 100       | 100      | 262/262                 | contig00021 | 54294  | 54555  | CP000858  | Plasmid    |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | IncI1        |                                   | 100       | 100      | 142/142                 | contig00017 | 3907   | 3766   | AP005147  | Plasmid    |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | blaTEM-57    | ampicillin                        | 99.88     | 100      | 861/861                 | contig00027 | 6176   | 5316   | FJ405211  | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid | 99.96     | 100      | 2637/2637               | contig00011 | 157768 | 160404 |           | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
-| SRR1952926 | tet(A)       | tetracycline                      | 99.92     | 97.8     | 1247/1275               | contig00027 | 1405   | 2651   | AF534183  | Resistance |
-+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
 resfinder.tsv
 `````````````
 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
++------------+--------+---------------------+---------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+-----------+-----------+
-| Isolate ID | Gene       | Predicted Phenotype  | %Identity  | %Overlap  | HSP Length/Total Length  | Contig       | Start  | End   | Accession |
+| Isolate ID | Gene   | Predicted Phenotype | CGE Predicted Phenotype   | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start | End  | Accession | Sequence  | CGE Notes |
-+============+============+======================+============+===========+==========================+==============+========+=======+===========+
++============+========+=====================+===========================+===========+==========+=========================+=============+=======+======+===========+===========+===========+
-| SRR1952908 | sul3       | sulfisoxazole        | 100.00     | 100.00    | 792/792                  | contig00030  | 2091   | 2882  | AJ459418  |
+| SRR1952908 | sul3   | sulfisoxazole       | Sulfamethoxazole          | 100.00    | 100.00   | 792/792                 | contig00030 | 2091  | 2882 | AJ459418  | ATGA[...] |           |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
+| SRR1952908 | tet(A) | tetracycline        | Doxycycline, Tetracycline | 99.92     | 97.80    | 1247/1275               | contig00032 | 1476  | 2722 | AF534183  | ATGT[...] |           |
-| SRR1952908 | tet(A)     | tetracycline         | 99.92      | 100.00    | 1200/1200                | contig00032  | 1551   | 2750  | AJ517790  |
++------------+--------+---------------------+---------------------------+-----------+----------+-------------------------+-------------+-------+------+-----------+-----------+-----------+
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
-| SRR1952908 | cmlA1      | chloramphenicol      | 99.92      | 100.00    | 1260/1260                | contig00030  | 6707   | 5448  | M64556    |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
-| SRR1952908 | aadA1      | streptomycin         | 100.00     | 100.00    | 792/792                  | contig00030  | 5355   | 4564  | JQ414041  |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
-| SRR1952908 | aadA2      | streptomycin         | 99.75      | 100.00    | 792/792                  | contig00030  | 7760   | 6969  | JQ364967  |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
-| SRR1952908 | blaTEM-57  | ampicillin           | 99.88      | 100.00    | 861/861                  | contig00032  | 6247   | 5387  | FJ405211  |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
-| SRR1952926 | tet(A)     | tetracycline         | 99.92      | 100.00    | 1200/1200                | contig00027  | 1480   | 2679  | AJ517790  |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
-| SRR1952926 | blaTEM-57  | ampicillin           | 99.88      | 100.00    | 861/861                  | contig00027  | 6176   | 5316  | FJ405211  |
-+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
 plasmidfinder.tsv
 `````````````````
 A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line.
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
++------------+-----------+-----------+----------+-------------------------+-------------+-------+------+-----------+
-| Isolate ID | Plasmid   | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start | End   | Accession |
+| Isolate ID | Plasmid   | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start | End  | Accession |
-+============+===========+===========+==========+=========================+=============+=======+=======+===========+
++============+===========+===========+==========+=========================+=============+=======+======+===========+
-| SRR1952908 | ColpVC    | 98.96     | 100      | 193/193                 | contig00038 | 1618  | 1426  | JX133088  |
+| SRR1952908 | ColpVC    | 98.96     | 100      | 193/193                 | contig00038 | 1618  | 1426 | JX133088  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
+| SRR1952908 | IncFIB(S) | 98.91     | 100      | 643/643                 | contig00024 | 10302 | 9660 | FN432031  |
-| SRR1952908 | IncFIB(S) | 98.91     | 100      | 643/643                 | contig00024 | 10302 | 9660  | FN432031  |
++------------+-----------+-----------+----------+-------------------------+-------------+-------+------+-----------+
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
-| SRR1952908 | IncFII(S) | 100       | 100      | 262/262                 | contig00024 | 54294 | 54555 | CP000858  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
-| SRR1952908 | IncI1     | 100       | 100      | 142/142                 | contig00020 | 3907  | 3766  | AP005147  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
-| SRR1952926 | ColpVC    | 98.96     | 100      | 193/193                 | contig00037 | 657   | 849   | JX133088  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
-| SRR1952926 | IncFIB(S) | 98.91     | 100      | 643/643                 | contig00021 | 10302 | 9660  | FN432031  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
-| SRR1952926 | IncFII(S) | 100       | 100      | 262/262                 | contig00021 | 54294 | 54555 | CP000858  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
-| SRR1952926 | IncI1     | 100       | 100      | 142/142                 | contig00017 | 3907  | 3766  | AP005147  |
-+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
 pointfinder.tsv
 ```````````````
 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
-+-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
++------------+-------------+-----------------------------------+------------------------------+-------+----------+---------------------+-----------+----------+-------------------------+-------------+--------+--------+----------------------+-----------+-----------------------+---------------------+------------------+
-| Isolate ID  | Gene         | Predicted Phenotype                | Type   | Position  | Mutation             | %Identity  | %Overlap  | HSP Length/Total Length  | Contig       | Start   | End    |
+| Isolate ID | Gene        | Predicted Phenotype               | CGE Predicted Phenotype      | Type  | Position | Mutation            | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start  | End    | Pointfinder Position | CGE Notes | CGE Required Mutation | CGE Mechanism       | CGE PMID         |
-+=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
++============+=============+===================================+==============================+=======+==========+=====================+===========+==========+=========================+=============+========+========+======================+===========+=======================+=====================+==================+
-| SRR1952908  | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid  | codon  | 83        | TCC -> TAC (S -> Y)  | 99.96      | 100.00    | 2637/2637                | contig00008  | 22801   | 20165  |
+| SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | Nalidixic acid,Ciprofloxacin | codon | 83       | TCC -> 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 |
-| SRR1952926  | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid  | codon  | 83        | TCC -> TAC (S -> Y)  | 99.96      | 100.00    | 2637/2637                | contig00011  | 157768  | 160404 |
++------------+-------------+-----------------------------------+------------------------------+-------+----------+---------------------+-----------+----------+-------------------------+-------------+--------+--------+----------------------+-----------+-----------------------+---------------------+------------------+
-+-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
 settings.txt
 ````````````
 The command-line, database versions, and other settings used to run `staramr`.
 ::
-command_line                  = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
+command_line                  = staramr search --pointfinder-organism enterococcus_faecium -o out pbp5.fa
-version                       = 0.7.1
+version                       = 0.10.0
-start_time                    = 2019-04-25 16:01:32
+start_time                    = 2023-08-23 13:37:41
-end_time                      = 2019-04-25 16:01:34
+end_time                      = 2023-08-23 13:37:42
-total_minutes                 = 0.04
+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           = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
+resfinder_db_commit           = fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd
-resfinder_db_date             = Mon, 16 Jul 2018 16:58
+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         = 8706a6363bb29e47e0e398c53043b037c24b99a7
+pointfinder_db_commit         = 8c694b9f336153e6d618b897b3b4930961521eb8
-pointfinder_db_date           = Wed, 04 Jul 2018 14:27
+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       = 81919954cbedaff39056610ab584ab4c06011ed8
+plasmidfinder_db_commit       = c18e08c17a5988d4f075fc1171636e47546a323d
-plasmidfinder_db_date         = Tue, 20 Nov 2018 08:51
+plasmidfinder_db_date         = Wed, 18 Jan 2023 09:45
-pointfinder_gene_drug_version = 050218
+mlst_version                  = 2.23.0
-resfinder_gene_drug_version   = 050218.1
+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.
-Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
+Galaxy wrapper written by Aaron Petkau and Eric Marinier at the National Microbiology Laboratory, Public Health Agency of Canada.
 .. _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

Mercurial > repos > nml > staramr

comparison staramr_search.xml @ 18:3b22de20bd4b draft default tip