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18 Commits
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| 72f7af1879 |
16
.devcontainer/Dockerfile
Normal file
16
.devcontainer/Dockerfile
Normal file
@@ -0,0 +1,16 @@
|
||||
FROM mcr.microsoft.com/devcontainers/miniconda:1-3
|
||||
|
||||
# Copy environment.yml (if found) to a temp location so we update the environment. Also
|
||||
# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
|
||||
COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
|
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RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
|
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&& rm -rf /tmp/conda-tmp
|
||||
|
||||
# [Optional] Uncomment to install a different version of Python than the default
|
||||
# RUN conda install -y python=3.6 \
|
||||
# && pip install --no-cache-dir pipx \
|
||||
# && pipx reinstall-all
|
||||
|
||||
# [Optional] Uncomment this section to install additional OS packages.
|
||||
# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
|
||||
# && apt-get -y install --no-install-recommends <your-package-list-here>
|
||||
@@ -3,7 +3,7 @@
|
||||
{
|
||||
"name": "Python 3",
|
||||
// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
|
||||
"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
|
||||
"image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
|
||||
|
||||
// Features to add to the dev container. More info: https://containers.dev/features.
|
||||
// "features": {},
|
||||
|
||||
3
.devcontainer/noop.txt
Normal file
3
.devcontainer/noop.txt
Normal file
@@ -0,0 +1,3 @@
|
||||
This file is copied into the container along with environment.yml* from the
|
||||
parent folder. This is done to prevent the Dockerfile COPY instruction from
|
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failing if no environment.yml is found.
|
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1
.gitignore
vendored
1
.gitignore
vendored
@@ -1,2 +1,3 @@
|
||||
galaxy-server/**
|
||||
test_results
|
||||
autobigs-cli_test_report.html
|
||||
|
||||
6
.gitmodules
vendored
Normal file
6
.gitmodules
vendored
Normal file
@@ -0,0 +1,6 @@
|
||||
[submodule "auto-updated-tools-iuc"]
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path = auto-updated-tools-iuc
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url = https://github.com/Syph-and-VPD-Lab/auto-updated-tools-iuc.git
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[submodule "galaxy"]
|
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path = galaxy
|
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url = https://github.com/galaxyproject/galaxy.git
|
||||
3
.vscode/extensions.json
vendored
3
.vscode/extensions.json
vendored
@@ -2,6 +2,7 @@
|
||||
"recommendations": [
|
||||
"mechatroner.rainbow-csv",
|
||||
"redhat.vscode-xml",
|
||||
"ms-vscode.live-server"
|
||||
"ms-vscode.live-server",
|
||||
"davelopez.galaxy-tools"
|
||||
]
|
||||
}
|
||||
6
.vscode/tasks.json
vendored
6
.vscode/tasks.json
vendored
@@ -6,19 +6,19 @@
|
||||
{
|
||||
"label": "lint",
|
||||
"type": "shell",
|
||||
"command": "planemo lint",
|
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"command": "planemo lint auto-updated-tools-iuc/tools/autobigs",
|
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"problemMatcher": []
|
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},
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{
|
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"label": "serve",
|
||||
"type": "shell",
|
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"command": "planemo serve",
|
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"command": "planemo serve auto-updated-tools-iuc/tools/autobigs --conda_channels https://git.reslate.systems/api/packages/ydeng/conda,bioconda,conda-forge",
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"problemMatcher": []
|
||||
},
|
||||
{
|
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"label": "run tests",
|
||||
"type": "shell",
|
||||
"command": "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html",
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"command": "planemo test auto-updated-tools-iuc/tools/autobigs/autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html --conda_channels https://git.reslate.systems/api/packages/ydeng/conda,bioconda,conda-forge",
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"problemMatcher": []
|
||||
}
|
||||
]
|
||||
|
||||
2
Jenkinsfile
vendored
2
Jenkinsfile
vendored
@@ -12,7 +12,7 @@ pipeline {
|
||||
steps {
|
||||
sh 'pip install -r requirements.txt'
|
||||
sh 'pip install standard-imghdr'
|
||||
sh 'useradd galaxy -m'
|
||||
sh 'planemo ci_setup'
|
||||
}
|
||||
}
|
||||
stage ("lint") {
|
||||
|
||||
17
README.md
Normal file
17
README.md
Normal file
@@ -0,0 +1,17 @@
|
||||
|
||||
# autoBIGS.Galaxy
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||||
|
||||
A program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. autoBIGS.galaxy is the galaxy frontend implementation of autoBIGS.cli and autoBIGS.engine.
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|
||||
This Galaxy tool implements [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine) via wrapping the official [autoBIGS.cli](https://github.com/Syph-and-VPD-Lab/autoBIGS.cli) wrapper.
|
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|
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## Features
|
||||
|
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This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine) is capable of:
|
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- Import multiple whole genome FASTA files
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- Fetch the available BIGSdb databases that is currently live and available
|
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- Fetch the available BIGSdb database schemas for a given MLST database
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- Retrieve exact/non-exact MLST allele variant IDs based off a sequence
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- Retrieve MLST sequence type IDs based off a sequence
|
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- Inexact matches are annotated with an asterisk (\*)
|
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- Output all results to a single CSV
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1
auto-updated-tools-iuc
Submodule
1
auto-updated-tools-iuc
Submodule
Submodule auto-updated-tools-iuc added at c2efa2b703
127
autobigs-cli.xml
127
autobigs-cli.xml
@@ -1,127 +0,0 @@
|
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<tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
|
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<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
|
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<macros>
|
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<token name="@TOOL_VERSION@">0.5.0</token>
|
||||
<token name="@VERSION_SUFFIX@">0</token>
|
||||
<import>autobigs-cli_macros.xml</import>
|
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<expand macro="bio_tools"/>
|
||||
</macros>
|
||||
|
||||
<requirements>
|
||||
<requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
|
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</requirements>
|
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|
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<command detect_errors="exit_code"><![CDATA[
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||||
#if $mode['operation'] == "info":
|
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#if $select_info['retrieved'] == "schemas":
|
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autoBIGS info $selected_schema --csv $info_db_out
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#else if $select_info['retrieved'] == "databases":
|
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autoBIGS info --retrieve-bigsdbs --csv $info_schemes_out
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#end if
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#else if $mode['operation'] == "st":
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autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
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#end if
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]]></command>
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<inputs>
|
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<conditional name="mode">
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<param name="operation" label="Operation" type="select">
|
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<option value="info">Retrieve Database Information</option>
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<option value="st">Perform Sequence Typing</option>
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</param>
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<when value="info">
|
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<conditional name="select_info">
|
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<param name="retrieved" label="Schemas or Database List" type="select">
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<option value="schemes">Available Schemas for Database</option>
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<option value="databases">Available Databases</option>
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</param>
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<when value="schemes">
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<repeat name="schemes_list" title="Schemes" min="1">
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<param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
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</repeat>
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</when>
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<when value="databases">
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|
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</when>
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</conditional>
|
||||
</when>
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||||
<when value="st">
|
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<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
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<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
|
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<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
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<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
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||||
</when>
|
||||
</conditional>
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</inputs>
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<outputs>
|
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<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
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<filter>mode['operation'] == "st"</filter>
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</data>
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<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
|
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<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter>
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||||
</data>
|
||||
<data name="info_schemes_out" label="${tool.name} supported Databases" format="csv">
|
||||
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'schemes'</filter>
|
||||
</data>
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||||
</outputs>
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||||
<tests>
|
||||
<test expect_num_outputs="1">
|
||||
<param name="operation" value="st" />
|
||||
<param name="fastas" value="tohama_I_bpertussis_wgs.fasta" />
|
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<param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
|
||||
<param name="schema" value="3" />
|
||||
<output name="mlst_profiles_output" file="tohama_I_bpertussis_wgs_typed.csv" ftype="csv" />
|
||||
</test>
|
||||
<test expect_num_outputs="1">
|
||||
<param name="operation" value="info" />
|
||||
<param name="retrieved" value="databases" />
|
||||
<output name="info_db_out">
|
||||
<assert_contents>
|
||||
<has_text text="BIGSdb Names,Source"/>
|
||||
<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
|
||||
</assert_contents>
|
||||
</output>
|
||||
</test>
|
||||
</tests>
|
||||
<help><![CDATA[
|
||||
|
||||
usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]]
|
||||
|
||||
Fetches the latest BIGSdb MLST database definitions.
|
||||
|
||||
options:
|
||||
-h, --help show this help message and exit
|
||||
--retrieve-bigsdbs Lists all known BIGSdb MLST databases (fetched from known APIs and cached).
|
||||
--retrieve-bigsdb-schemas SCHEMA_IDS
|
||||
Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given.
|
||||
|
||||
usage: autoBIGS st [-h] [--exact] [--stop-on-fail] fastas [fastas ...] seqdefdb schema out
|
||||
|
||||
Returns MLST exact profile matches.
|
||||
|
||||
positional arguments:
|
||||
fastas The FASTA files to process. Multiple can be listed.
|
||||
seqdefdb The BIGSdb seqdef database to use for typing.
|
||||
schema The BIGSdb seqdef database schema ID (integer) to use for typing.
|
||||
out The output CSV name (.csv will be appended).
|
||||
|
||||
options:
|
||||
-h, --help show this help message and exit
|
||||
--stop-on-fail, -sof Should the algorithm stop in the case there are no matches (or partial matches when
|
||||
expecting exact matches).
|
||||
|
||||
|
||||
]]></help>
|
||||
<citations>
|
||||
<citation type="bibtex">
|
||||
@book{Deng2025RealYHD,
|
||||
title = {Syph-and-VPD-Lab/autoBIGS.cli},
|
||||
url = {https://github.com/Syph-and-VPD-Lab/autoBIGS.cli},
|
||||
author = {Deng, Harrison},
|
||||
date = {2025-01-24},
|
||||
year = {2025},
|
||||
month = {1},
|
||||
day = {24},
|
||||
}
|
||||
</citation>
|
||||
</citations>
|
||||
</tool>
|
||||
@@ -1,7 +0,0 @@
|
||||
<macros>
|
||||
<xml name="bio_tools">
|
||||
<xrefs>
|
||||
<xref type="bio.tools">AutoBIGS.CLI</xref>
|
||||
</xrefs>
|
||||
</xml>
|
||||
</macros>
|
||||
7
environment.yml
Normal file
7
environment.yml
Normal file
@@ -0,0 +1,7 @@
|
||||
name: base
|
||||
channels:
|
||||
- bioconda
|
||||
- conda-forge
|
||||
dependencies:
|
||||
- python==3.12
|
||||
- planemo
|
||||
1
galaxy
Submodule
1
galaxy
Submodule
Submodule galaxy added at d416517709
@@ -1,146 +0,0 @@
|
||||
BIGSdb Names,Source
|
||||
pubmlst_aactinomycetemcomitans_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_abaumannii_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_achromobacter_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_aeromonas_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_afumigatus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_aparagallinarum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_aphagocytophilum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_arcobacter_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bbacilliformis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bcc_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bcereus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bfragilis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bhenselae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_blastocystis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_blicheniformis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bmallei_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api
|
||||
pubmlst_borrelia_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bpseudomallei_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_brachyspira_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_brucella_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bsubtilis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_bwashoensis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_calbicans_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_campylobacter_nonjejuni_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_campylobacter_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cbotulinum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cchauvoei_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cdifficile_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cfreundii_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cglabrata_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_chlamydiales_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ckrusei_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cmaltaromaticum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cperfringens_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_cronobacter_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_csepticum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_csinensis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ctropicalis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_diphtheria_seqdef,https://bigsdb.pasteur.fr/api
|
||||
pubmlst_dnodosus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ecloacae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_edwardsiella_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_efaecalis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_efaecium_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_escherichia_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_fpsychrophilum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_gallibacterium_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_geotrichum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_hcinaedi_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_helicobacter_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_hinfluenzae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_hparasuis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_hsuis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_kaerogenes_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_klebsiella_seqdef,https://bigsdb.pasteur.fr/api
|
||||
pubmlst_koxytoca_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_kseptempunctata_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_leptospira_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_lgarvieae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_liberibacter_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_listeria_seqdef,https://bigsdb.pasteur.fr/api
|
||||
pubmlst_llactis_phage_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_lsalivarius_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mabscessus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_magalactiae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_manserisalpingitidis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mbovis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mcanis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mcaseolyticus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mflocculare_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mgallisepticum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mgenitalium_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mhaemolytica_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mhominis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mhyopneumoniae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mhyorhinis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mhyosynoviae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_miowae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mplutonius_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mpneumoniae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_msciuri_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_msynoviae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_mycobacteria_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_neisseria_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_oralstrep_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_orhinotracheale_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_otsutsugamushi_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_pacnes_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_paeruginosa_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_pdamselae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_pfluorescens_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_pgingivalis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_plarvae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_plasmid_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_pmultocida_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ppentosaceus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_pputida_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_proteus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_psalmonis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ranatipestifer_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_rhodococcus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_rmlst_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sagalactiae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_salmonella_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_saureus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sbsec_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_scanis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_schromogenes_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sdysgalactiae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sepidermidis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_serratia_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sgallolyticus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_shaemolyticus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_shewanella_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_shominis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_siniae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sinorhizobium_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_smaltophilia_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_smitis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sparasitica_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_spneumoniae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_spseudintermedius_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_spyogenes_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ssuis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_sthermophilus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_streptomyces_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_suberis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_szooepidemicus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_taylorella_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_tenacibaculum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_test_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_tpallidum_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_tvaginalis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_ureaplasma_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_vcholerae_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_vibrio_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_vparahaemolyticus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_vtapetis_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_vvulnificus_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_wolbachia_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_xcitri_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_xfastidiosa_seqdef,https://rest.pubmlst.org
|
||||
pubmlst_yersinia_seqdef,https://bigsdb.pasteur.fr/api
|
||||
pubmlst_yruckeri_seqdef,https://rest.pubmlst.org
|
||||
|
@@ -1,11 +0,0 @@
|
||||
Name,ID
|
||||
Autotransporters,11
|
||||
Bp_vaccine antigens,7
|
||||
MLST,3
|
||||
Other toxins,9
|
||||
PRN-test-Bp,5
|
||||
Phase,8
|
||||
T3SS,10
|
||||
cgMLST_genus,1
|
||||
cgMLST_pertussis,4
|
||||
macrolide resistance,6
|
||||
|
File diff suppressed because it is too large
Load Diff
@@ -1,2 +0,0 @@
|
||||
id,st,clonal-complex,adk,fumC,glyA,icd,pepA,pgm,tyrB
|
||||
BX470248.1,1,ST-2 complex,1,1,1,1,1,1,1
|
||||
|
Reference in New Issue
Block a user