Mercurial > repos > iuc > data_manager_build_coreprofiler
changeset 1:a95177c4d627 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit ed6d188035ac31aa2da132889141b0898aa6bc86
| author | iuc |
|---|---|
| date | Fri, 21 Nov 2025 13:12:00 +0000 |
| parents | c3553950db1b |
| children | |
| files | README.rst data_manager/data_manager_build_coreprofiler_download.xml test-data/coreprofiler_scheme.loc.test |
| diffstat | 3 files changed, 261 insertions(+), 22 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Nov 21 13:12:00 2025 +0000 @@ -0,0 +1,90 @@ +This tool downloads and builds the **CoreProfiler** scheme. +------------------------------------------------------------------------------- + +You can find the list of available schemes, as well as the reference platforms supported by CoreProfiler, in the +`CoreProfiler documentation <https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md?ref_type=heads#basic-usage>`_. + +Please refer to this page for details on how to use the tool and which schema options are available. + +Use Galaxy's data manager framework to download and install new CoreProfiler schemes. + +If you want to use a scheme from **EnteroBase**, you do not need to provide any token or secret. + +However, if you want to use a scheme from **pubMLST** or **BigsDB**, you will need to follow a procedure before launching the data manager. + +BIGSdb and PubMLST platforms require **OAuth1 authentication** to access and download the most up-to-date schemes. +While authentication is not strictly mandatory, skipping it may result in downloading outdated schemes. + +This authentication involves two types of tokens: + +* **Consumer tokens**: permanent tokens used to initiate the authentication flow. +* **Access tokens**: tokens required to download a scheme. + +Procedure for **pubMLST schemes** (example: ``borrelia_3-cgMLST-639-pubmlst``) +------------------------------------------------------------------------------- + +1. Create an account on the `pubMLST website <https://pubmlst.org/bigsdb>`_. +2. Generate a consumer token and secret from your account settings + (**My account → API keys → Enter key name → Submit**). +3. On your account page, go to **Database registrations**, check all databases, and register. +4. Download `coreprofiler <https://gitlab.com/ifb-elixirfr/abromics/coreprofiler>`_ locally and run the following command to obtain your access token and secret: + + .. code-block:: bash + + coreprofiler db get_request_tokens --scheme <SCHEME_NAME> \ + --consumer_key <YOUR_CONSUMER_TOKEN> \ + --consumer_secret <YOUR_CONSUMER_SECRET> + + Replace the placeholders with your scheme of interest (example: ``borrelia_3``) and your actual consumer token and secret. + + This command will provide you with a URL to visit in order to authorize the client software to access your account. + After authorizing, it will give you a verification code that you need to enter in the command line prompt. + It will then return your access token and secret. + +5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool + by setting these bash variables in a ``.txt`` file: + + .. code-block:: bash + + export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>" + export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>" + export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>" + export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>" + +6. Set the path to this ``.txt`` file in your environment by making an environment variable + (example: ``export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"``). + + +Procedure for **BigsDB schemes** (example: ``bordetella_1-cgMLST_genus-1415-BIGSdb``) +-------------------------------------------------------------------------------------- + +1. Create an account on the `BigsDB website <https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?page=registration>`_. +2. Ask for a consumer token and secret by sending an email to ``bigsdb@pasteur.fr`` + (subject: **API client key**). +3. On your account page, go to **Database registrations**, check all databases, and register. +4. Download `coreprofiler <https://gitlab.com/ifb-elixirfr/abromics/coreprofiler>`_ locally and run the following command to obtain your access token and secret: + + .. code-block:: bash + + coreprofiler db get_request_tokens --scheme <SCHEME_NAME> \ + --consumer_key <YOUR_CONSUMER_TOKEN> \ + --consumer_secret <YOUR_CONSUMER_SECRET> + + Replace the placeholders with your scheme of interest (example: ``bordetella_1``) and your actual consumer token and secret. + + This command will provide you with a URL to visit in order to authorize the client software to access your account. + After authorizing, it will give you a verification code that you need to enter in the command line prompt. + It will then return your access token and secret. + +5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool + by setting these bash variables in a ``.txt`` file: + + .. code-block:: bash + + export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>" + export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>" + export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>" + export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>" + +6. Set the path to this ``.txt`` file in your environment by making an environment variable + (example: ``export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"``).
--- a/data_manager/data_manager_build_coreprofiler_download.xml Tue Jul 22 09:00:12 2025 +0000 +++ b/data_manager/data_manager_build_coreprofiler_download.xml Fri Nov 21 13:12:00 2025 +0000 @@ -1,7 +1,7 @@ <tool id="data_manager_build_coreprofiler" name="Download and build CoreProfiler scheme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@"> <description></description> <macros> - <token name="@TOOL_VERSION@">1.1.3</token> + <token name="@TOOL_VERSION@">1.1.7</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <xml name="version_command"> @@ -28,20 +28,46 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ #set $scheme_name = str($coreprofiler_scheme_select).split('-')[0] +#set $scheme_db = str($coreprofiler_scheme_select).split('-')[3] + +#set $db_version = str($db_version) mkdir -p '$out_file.extra_files_path' && -mkdir -p coreprofiler_${scheme_name}/scheme_$scheme_name/ && - -coreprofiler db download - -s $scheme_name - -o coreprofiler_${scheme_name}/scheme_$scheme_name && +mkdir -p coreprofiler_${scheme_name}_${db_version}/scheme_$scheme_name/ && +#if $db_version == "token_version" + source "$COREPROFILER_SECRETS_PATH" && + if [[ -z "$COREPROFILER_CONSUMER_TOKEN" || -z "$COREPROFILER_CONSUMER_SECRET" || -z "$COREPROFILER_ACCESS_TOKEN" || -z "$COREPROFILER_ACCESS_SECRET" ]]; then + echo "Error: Missing required bash variables for CoreProfiler authentication." >&2 + echo "Please set the following variables before running this tool:" >&2 + echo " COREPROFILER_CONSUMER_TOKEN" >&2 + echo " COREPROFILER_CONSUMER_SECRET" >&2 + echo " COREPROFILER_ACCESS_TOKEN" >&2 + echo " COREPROFILER_ACCESS_SECRET" >&2 + echo "Please refer to the data manager help section for more information on how to generate these tokens." >&2 + fi && +#end if + coreprofiler db download + -s $scheme_name + -o coreprofiler_${scheme_name}_${db_version}/scheme_$scheme_name + ## Used only for test + #if str($hide_test) == 'true': + -t + #end if + ## +#if $db_version == "token_version" + -k "$COREPROFILER_CONSUMER_TOKEN" + -ks "$COREPROFILER_CONSUMER_SECRET" + -a "$COREPROFILER_ACCESS_TOKEN" + -as "$COREPROFILER_ACCESS_SECRET" +#end if +&& coreprofiler db makeblastdb - -s coreprofiler_${scheme_name}/scheme_$scheme_name + -s coreprofiler_${scheme_name}_${db_version}/scheme_$scheme_name -n $scheme_name - -p coreprofiler_${scheme_name}/db_$scheme_name && + -p coreprofiler_${scheme_name}_${db_version}/db_$scheme_name && -mv coreprofiler_${scheme_name} '$out_file.extra_files_path' && +mv coreprofiler_${scheme_name}_${db_version} '$out_file.extra_files_path' && cp '$dmjson' '$out_file' ]]></command> @@ -54,21 +80,30 @@ #set $scheme_loci = str($coreprofiler_scheme_select).split('-')[2] #set $scheme_db = str($coreprofiler_scheme_select).split('-')[3] +#set $db_version = str($db_version) + { "data_tables":{ "coreprofiler_scheme":[ { - "value": "coreprofiler_downloaded_#echo date.today().strftime('%d%m%Y')#-${scheme_name}-${scheme_desc}-${scheme_loci}-${scheme_db}", - "name": "${scheme_name}: ${scheme_desc} [${scheme_loci} loci] (${scheme_db})", - "path": "coreprofiler_${scheme_name}", - "database": "coreprofiler_${scheme_name}/db_${scheme_name}/${scheme_name}.fasta", - "scheme": "coreprofiler_${scheme_name}/scheme_${scheme_name}" + "value": "coreprofiler_downloaded_#echo date.today().strftime('%d%m%Y')#-${scheme_name}-${scheme_desc}-${scheme_loci}-${scheme_db}-${db_version}", + "name": "${scheme_name}: ${scheme_desc} [${scheme_loci} loci] (${scheme_db}-${db_version})", + "path": "coreprofiler_${scheme_name}_${db_version}", + "database": "coreprofiler_${scheme_name}_${db_version}/db_${scheme_name}/${scheme_name}.fasta", + "scheme": "coreprofiler_${scheme_name}_${db_version}/scheme_${scheme_name}" } ] } }]]></configfile> </configfiles> <inputs> + <param name="db_version" type="select" label="Select if you want latest version from pubMLST or BigsDB using tokens" help="If you choose latest, you will have to provide tokens and secrets to access the database following the procedure describe in the documentation." > + <option value="token" selected="true">Latest version from pubMLST or BigsDB, you will need to set bash variables for tokens and secrets as described in the documentation.</option> + <option value="no_token">No need of tokens but it will download the previous version, not the latest version, from pubMLST or BigsDB or if you want a database from Enterobase</option> + </param> + <!-- used only for tests, limit download scheme to 50 locus --> + <param name="hide_test" type="hidden" value=""/> + <!-- --> <param name="coreprofiler_scheme_select" type="select" label="CoreProfiler available scheme" help="Choose a schema from a reference platform supported in CoreProfiler"> <option value="bordetella_1-cgMLST_genus-1415-BIGSdb">bordetella_1: cgMLST_genus [1415 loci] (BIGSdb)</option> <option value="bordetella_4-cgMLST_pertussis-2038-BIGSdb">bordetella_4: cgMLST_pertussis [2038 loci] (BIGSdb)</option> @@ -98,7 +133,7 @@ <option value="cchauvoei_1-cgMLST-2223-pubmlst">cchauvoei_1: cgMLST [2223 loci] (pubmlst)</option> <option value="cperfringens_2-cgMLST-1431-pubmlst">cperfringens_2: cgMLST [1431 loci] (pubmlst)</option> <option value="dnodosus_3-cgMLST-714-pubmlst">dnodosus_3: cgMLST [714 loci] (pubmlst)</option> - <option value="escherichia_6-cgMLST-2513-pubmlst">escherichia_6: cgMLST [2513 loci] (pubmlst)</option> + <option value="escherichia_v1-cgMLST-2513-enterobase">escherichia_v1: cgMLST v1 [2513 loci] (enterobase)</option> <option value="hinfluenzae_56-cgMLST_v1-1037-pubmlst">hinfluenzae_56: cgMLST v1 [1037 loci] (pubmlst)</option> <option value="leptospira_4-cgMLST-1565-pubmlst">leptospira_4: cgMLST [1565 loci] (pubmlst)</option> <option value="mabscessus_2-cgMLST-2904-pubmlst">mabscessus_2: cgMLST [2904 loci] (pubmlst)</option> @@ -111,7 +146,7 @@ <option value="neisseria_85-N._meningitidis_cgMLST_v2-1422-pubmlst">neisseria_85: N. meningitidis cgMLST v2 [1422 loci] (pubmlst)</option> <option value="neisseria_88-N._meningitidis_cgMLST_v3-1329-pubmlst">neisseria_88: N. meningitidis cgMLST v3 [1329 loci] (pubmlst)</option> <option value="pmultocida_3-cgMLST_draft_1233-pubmlst">pmultocida_3: cgMLST (draft) [1233 loci] (pubmlst)</option> - <option value="salmonella_4-cgMLST_v2_Enterobase-3002-pubmlst">salmonella_4: cgMLST v2 (Enterobase) [3002 loci] (pubmlst)</option> + <option value="salmonella_v2-cgMLST-3002-enterobase">salmonella_v2: cgMLST v2 [3002 loci] (enterobase)</option> <option value="salmonella_3-SalmcgMLST_v1.0-2750-pubmlst">salmonella_3: SalmcgMLST v1.0 [2750 loci] (pubmlst)</option> <option value="serratia_2-cgMLST-2692-pubmlst">serratia_2: cgMLST [2692 loci] (pubmlst)</option> <option value="saureus_20-cgMLST-1716-pubmlst">saureus_20: cgMLST [1716 loci] (pubmlst)</option> @@ -128,15 +163,47 @@ </outputs> <tests> <test expect_num_outputs="1"> + <param name="hide_test" value="true"/> <param name="coreprofiler_scheme_select" value="borrelia_3-cgMLST-639-pubmlst" /> + <param name="db_version" value="no_token"/> + <output name="out_file"> + <assert_contents> + <has_text text='"coreprofiler_scheme":'/> + <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-borrelia_3-cgMLST-639-pubmlst-no_token"'/> + <has_text text='"name": "borrelia_3: cgMLST [639 loci] (pubmlst-no_token)"'/> + <has_text text='"path": "coreprofiler_borrelia_3_no_token"'/> + <has_text text='"database": "coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta"'/> + <has_text text='"scheme": "coreprofiler_borrelia_3_no_token/scheme_borrelia_3"'/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="hide_test" value="true"/> + <param name="coreprofiler_scheme_select" value="yersinia_1-Yersinia_cgMLST-500-BIGSdb" /> + <param name="db_version" value="no_token"/> <output name="out_file"> <assert_contents> <has_text text='"coreprofiler_scheme":'/> - <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-borrelia_3-cgMLST-639-pubmlst"'/> - <has_text text='"name": "borrelia_3: cgMLST [639 loci] (pubmlst)'/> - <has_text text='"path": "coreprofiler_borrelia_3"'/> - <has_text text='"database": "coreprofiler_borrelia_3/db_borrelia_3/borrelia_3.fasta"'/> - <has_text text='"scheme": "coreprofiler_borrelia_3/scheme_borrelia_3"'/> + <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token"'/> + <has_text text='"name": "yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)"'/> + <has_text text='"path": "coreprofiler_yersinia_1_no_token"'/> + <has_text text='"database": "coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta"'/> + <has_text text='"scheme": "coreprofiler_yersinia_1_no_token/scheme_yersinia_1"'/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="hide_test" value="true"/> + <param name="coreprofiler_scheme_select" value="escherichia_v1-cgMLST-2513-enterobase" /> + <param name="db_version" value="no_token"/> + <output name="out_file"> + <assert_contents> + <has_text text='"coreprofiler_scheme":'/> + <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-escherichia_v1-cgMLST-2513-enterobase-no_token"'/> + <has_text text='"name": "escherichia_v1: cgMLST [2513 loci] (enterobase-no_token)"'/> + <has_text text='"path": "coreprofiler_escherichia_v1_no_token"'/> + <has_text text='"database": "coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta"'/> + <has_text text='"scheme": "coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1"'/> </assert_contents> </output> </test> @@ -147,6 +214,81 @@ You can find the list of available scheme, as well as the reference platforms supported by CoreProfiler, in the <a href="https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md?ref_type=heads#basic-usage" target="_blank">CoreProfiler documentation</a>. Please refer to this page for details on how to use the tool and which schema options are available. + +Use Galaxy's data manager framework to download and install new CoreProfiler schemes : + +If you want to use a scheme from enterobase, you do not need to provide any token or secret. + +However, if you want to use a scheme from **pubMLST** or **BigsDB**, you will need to follow a procedure before launching the data manager. + +BIGSdb and PubMLST platforms require OAuth1 authentication to access and download the most up-to-date schemes. +While authentication is not strictly mandatory, skipping it may result in downloading outdated schemes. + +This authentication involves two types of tokens: + + * Consumer tokens : permanent tokens used to initiate the authentication flow. + + * Access tokens : tokens required to download a scheme. + +Procedure for pubMLST schemes (example with borrelia_3-cgMLST-639-pubmlst) : + +1. Create an account on the <a href="https://pubmlst.org/bigsdb" target="_blank">pubMLST</a> website. +2. Generate a consumer token and secret from your account settings (My account > API keys > Enter key name > Submit). +3. On your account page, go to Database registrations, check all databases and register. +4. Download <a href="https://gitlab.com/ifb-elixirfr/abromics/coreprofiler" target="_blank">coreprofiler</a> locally and run the following command to obtain your access token and secret + +Replace the placeholders with your scheme of interest (example : borrelia_3) your actual consumer token and secret : + +""" +coreprofiler db get_request_tokens --scheme <SCHEME_NAME> --consumer_key <YOUR_CONSUMER_TOKEN> --consumer_secret <YOUR_CONSUMER_SECRET> +""" + +This command will provide you with a URL to visit in order to authorize client software to access your account. + +After authorizing, it will give you a verification code that you need to enter in the command line prompt. + +It will then return your access token and secret. + +5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool by setting this bash variables in a txt file : + +""" +export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>" +export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>" +export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>" +export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>" +""" + +6. Set the path to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"). + +Procedure for BigsDB (example with bordetella_1-cgMLST_genus-1415-BIGSdb): + +1. Create an account on the <a href="https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?page=registration" target="_blank">BigsDB</a> website. +2. Ask for a consumer token and secret by sending a mail to bigsdb@pasteur.fr (object "API client key"). +3. On your account page, go to Database registrations, check all databases and register. +4. Download <a href="https://gitlab.com/ifb-elixirfr/abromics/coreprofiler" target="_blank">coreprofiler</a> locally and run the following command to obtain your access token and secret + +Replace the placeholders with your scheme of interest (example : bordetella_1) your actual consumer token and secret : + +""" +coreprofiler db get_request_tokens --scheme <SCHEME_NAME> --consumer_key <YOUR_CONSUMER_TOKEN> --consumer_secret <YOUR_CONSUMER_SECRET> +""" + +This command will provide you with a URL to visit in order to authorize client software to access your account. + +After authorizing, it will give you a verification code that you need to enter in the command line prompt. + +It will then return your access token and secret. + +5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool by setting this bash variables in a txt file : + +""" +export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>" +export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>" +export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>" +export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>" +""" + +6. Set the path to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt"). ]]></help> <citations> <citation type="doi">10.3390/microorganisms10020292</citation>
--- a/test-data/coreprofiler_scheme.loc.test Tue Jul 22 09:00:12 2025 +0000 +++ b/test-data/coreprofiler_scheme.loc.test Fri Nov 21 13:12:00 2025 +0000 @@ -8,4 +8,11 @@ # #For example #coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb klebsiella_3: scgMLST634 [632 loci] (BIGSdb) coreprofiler_klebsiella_3 coreprofiler_klebsiella_3/db_klebsiella_3/klebsiella_3.fasta coreprofiler_klebsiella_3/scheme_klebsiella_3 -coreprofiler_downloaded_10072025-borrelia_3-cgMLST-639-pubmlst borrelia_3: cgMLST [639 loci] (pubmlst) /tmp/tmpi2v1t1zz/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3 coreprofiler_borrelia_3/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3/scheme_borrelia_3 +coreprofiler_downloaded_10102025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmphn3k3ekk/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 +coreprofiler_downloaded_10102025-bordetella_1-cgMLST_genus-1415-BIGSdb-no_token bordetella_1: cgMLST_genus [1415 loci] (BIGSdb-no_token) /tmp/tmphn3k3ekk/galaxy-dev/tool-data/coreprofiler/coreprofiler_bordetella_1_no_token coreprofiler_bordetella_1_no_token/db_bordetella_1/bordetella_1.fasta coreprofiler_bordetella_1_no_token/scheme_bordetella_1 +coreprofiler_downloaded_28102025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmpomzcgw6j/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_17112025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmphe1udqum/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_17112025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmphe1udqum/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1 +coreprofiler_downloaded_17112025-borrelia_3-cgMLST-639-pubmlst-no_token borrelia_3: cgMLST [639 loci] (pubmlst-no_token) /tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta coreprofiler_borrelia_3_no_token/scheme_borrelia_3 +coreprofiler_downloaded_17112025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token) /tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta coreprofiler_yersinia_1_no_token/scheme_yersinia_1 +coreprofiler_downloaded_17112025-escherichia_v1-cgMLST-2513-enterobase-no_token escherichia_v1: cgMLST [2513 loci] (enterobase-no_token) /tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1