Updated shed file and added README

shedfile now passes planemo linting

.devcontainer/Dockerfile

@@ -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/
+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 \
+    && 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>

.devcontainer/devcontainer.json

@@ -1,9 +1,11 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/python
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
 {
-	"name": "Python 3",
+	"name": "Miniconda (Python 3)",
-	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"build": { 
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	}
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -12,7 +14,7 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt"
+	// "postCreateCommand": "python --version",
 
 	// Configure tool-specific properties.
 	// "customizations": {},

.devcontainer/noop.txt

@@ -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 
+failing if no environment.yml is found.

.gitignore

@@ -1,2 +1,2 @@
-autobigs-cli_test_report.html
 galaxy-server/**
+test_results

.shed.yml

@@ -0,0 +1,12 @@
+name: autobigs
+owner: ydeng
+description: Automated MLST typing from PubMLST and InstitutPasteur.
+homepage_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli
+long_description: |
+  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.
+remote_repository_url: https://github.com/Syph-and-VPD-Lab/autoBIGS.cli
+categories:
+- Sequence Analysis

.vscode/extensions.json

@@ -1,6 +1,5 @@
 {
     "recommendations": [
-        "davelopez.galaxy-tools",
         "mechatroner.rainbow-csv",
         "redhat.vscode-xml",
         "ms-vscode.live-server"

.vscode/tasks.json

@@ -8,6 +8,18 @@
             "type": "shell",
             "command": "planemo lint",
             "problemMatcher": []
+        },
+        {
+            "label": "serve",
+            "type": "shell",
+            "command": "planemo serve",
+            "problemMatcher": []
+        },
+        {
+            "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",
+            "problemMatcher": []
         }
     ]
 }

Jenkinsfile

@@ -0,0 +1,32 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'miniforge3'
+            inheritFrom 'miniforge'
+        }
+    }
+    
+    stages {
+        stage ("install") {
+            steps {
+                sh 'conda env update -n base --file environment.yml'
+                sh 'useradd galaxy -m'
+                sh 'apt-get update'
+                sh 'apt-get install sudo -y'
+            }
+        }
+        stage ("lint") {
+            steps {
+                sh "sudo -u galaxy planemo lint autobigs-cli.xml"
+            }
+        }
+        stage ("test") {
+            steps {
+                sh 'sudo -u galaxy mkdir test_results'
+                sh "sudo -u galaxy 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"
+                xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
+            }
+        }
+    }
+}

README.md

@@ -0,0 +1,17 @@
+
+# autoBIGS.Galaxy
+
+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.
+
+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.
+
+## Features
+
+This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine) is capable of:
+- Import multiple whole genome FASTA files
+- Fetch the available BIGSdb databases that is currently live and available
+- Fetch the available BIGSdb database schemas for a given MLST database
+- Retrieve exact/non-exact MLST allele variant IDs based off a sequence
+- Retrieve MLST sequence type IDs based off a sequence
+- Inexact matches are annotated with an asterisk (\*)
+- Output all results to a single CSV

autobigs-cli.xml

@@ -1,7 +1,7 @@
-<tool id="autobigs-cli" name="AutoBIGS.CLI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
 	<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
 	<macros>
-		<token name="@TOOL_VERSION@">0.4.3</token>
+		<token name="@TOOL_VERSION@">0.5.0</token>
 		<token name="@VERSION_SUFFIX@">0</token>
     	<import>autobigs-cli_macros.xml</import>
 	    <expand macro="bio_tools"/>
@@ -12,72 +12,107 @@
 	</requirements>
 
 	<command detect_errors="exit_code"><![CDATA[
-			#if $operation == "info":
+			#if $mode.operation == "info":
-				#if $retrieved == "schema":
+				#if $mode.select_info.retrieved == "schemes":
-					autoBIGS info $selected_schema
+					autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_schemes_out
-				#else if $retrieved == "databases":
+				#else if $mode.select_info.retrieved == "databases":
-					autoBIGS info --retrieve-bigsdbs
+					autoBIGS info --retrieve-bigsdbs --csv $info_db_out
 				#end if
-			#else if $operation == "st":
+			#else if $mode.operation == "st":
-				autoBIGS st $fastas $seqdefdb $schema $mlst_profiles_output
+				autoBIGS st#for $fasta in $mode.fastas_list# '${fasta.fasta}' #end for#"$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
 			#end if
 	]]></command>
 	<inputs>
 		<conditional name="mode">
 			<param name="operation" label="Operation" type="select">
-				<option value="info"/>
+				<option value="info">Retrieve Database Information</option>
-				<option value="st"/>
+				<option value="st">Perform Sequence Typing</option>
 			</param>
 			<when value="info">
-				<conditional name="select-info">
+				<conditional name="select_info">
-					<param name="retrieved" label="Schema or Database List" type="select">
+					<param name="retrieved" label="Schemes or Database List" type="select">
-						<option value="schema"/>
+						<option value="schemes">Available Schemas for Database</option>
-						<option value="databases"/>
+						<option value="databases">Available Databases</option>
 					</param>
-					<when value="schema">
+					<when value="schemes">
-						<repeat name="schemas" title="Schemas">
+						<repeat name="schemes_list" title="Schemes" min="1">
-							<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="integer" min="0"/>
+							<param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
 						</repeat>
 					</when>
-                    <when value="databases">
+					<when value="databases">
-                    <!-- No need to do anything -->
+
-                    </when>
+					</when>
 				</conditional>
 			</when>
 			<when value="st">
-				<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
+				<repeat name="fastas_list" title="Fasta" min="1">
-				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text"/>
+					<param name="fasta" label="FASTA file" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
+				</repeat>
+				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
 				<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
+				<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
 			</when>
 		</conditional>
 	</inputs>
 	<outputs>
 		<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
-			<filter>mode == "st"</filter>
+			<filter>mode['operation'] == 'st'</filter>
+		</data>
+		<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
+			<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
+		</data>
+		<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
+			<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
 		</data>
 	</outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="operation" value="st" />
-            <param name="fastas" value="tohama_I_bpertussis.fasta" />
+			<repeat name="fastas_list">
+	            <param name="fasta" value="tohama_I_bpertussis_wgs.fasta" />
+			</repeat>
             <param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
             <param name="schema" value="3" />
-            <output name="mlst_profiles_output" file="results.csv" ftype="csv" />
+            <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>
+        <test expect_num_outputs="1">
+            <param name="operation" value="info" />
+			<repeat name="schemes_list">
+            	<param name="selected_db" value="pubmlst_bordetella_seqdef" />
+			</repeat>
+            <output name="info_schemes_out">
+				<assert_contents>
+					<has_text text="Name,ID"/>
+					<has_text text="MLST,3"/>
+				</assert_contents>
+			</output>
         </test>
     </tests>
 	<help><![CDATA[
 
-usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]]
+usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]] [--csv CSV_OUTPUT]
 
 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-bigsdbs, -l
-  --retrieve-bigsdb-schemas SCHEMA_IDS
+                        Lists all known BIGSdb MLST databases (fetched from known APIs and cached).
+  --retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS
                         Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given.
+  --csv, -o CSV_OUTPUT  Output list as CSV at a given path. A suffix is added depending on the action taken.
 
-usage: autoBIGS st [-h] [--exact] [--stop-on-fail] fastas [fastas ...] seqdefdb schema out
+usage: autoBIGS st [-h] [--stop-on-fail] fastas [fastas ...] seqdefdb schema out
 
 Returns MLST exact profile matches.
 
@@ -89,17 +124,13 @@ positional arguments:
 
 options:
   -h, --help            show this help message and exit
-  --exact, -ex          Should run exact matching rather than returning all similar ones
+  --stop-on-fail, -sof  Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches).
-  --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 = {RealYHD/autoBIGS.cli},
+title = {Syph-and-VPD-Lab/autoBIGS.cli},
-url = {https://github.com/RealYHD/autoBIGS.cli},
+url = {https://github.com/Syph-and-VPD-Lab/autoBIGS.cli},
 author = {Deng, Harrison},
 date = {2025-01-24},
 year = {2025},

environment.yml

@@ -0,0 +1,7 @@
+name: base
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - python==3.12
+  - planemo

test-data/databases-2025-02-21.csv

@@ -0,0 +1,146 @@
+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

test-data/results.csv

@@ -1,2 +0,0 @@
-id,st,clonal-complex,tyrB,icd,pepA,adk,pgm,fumC,glyA
-BX470248.1,1,ST-2 complex,1,1,1,1,1,1,1

test-data/schemas-2025-02-21.csv

@@ -0,0 +1,11 @@
+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

test-data/tohama_I_bpertussis_wgs_typed.csv

@@ -0,0 +1,2 @@
+id,st,clonal-complex,adk,fumC,glyA,icd,pepA,pgm,tyrB
+BX470248.1,1,ST-2 complex,1,1,1,1,1,1,1