Initial work on wrapping AutoBIGS for Galaxy

.devcontainer/devcontainer.json

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+// 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
+{
+	"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",
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "pip3 install --user -r requirements.txt"
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.gitignore

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+autobigs-cli_test_report.html
+galaxy-server

.vscode/extensions.json

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+{
+    "recommendations": [
+        "davelopez.galaxy-tools",
+        "mechatroner.rainbow-csv",
+        "redhat.vscode-xml",
+        "ms-vscode.live-server"
+    ]
+}

.vscode/settings.json

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+{
+    "galaxyTools.planemo.galaxyRoot": "galaxy-server"
+}

.vscode/tasks.json

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+{
+    // See https://go.microsoft.com/fwlink/?LinkId=733558
+    // for the documentation about the tasks.json format
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "lint",
+            "type": "shell",
+            "command": "planemo lint",
+            "problemMatcher": []
+        }
+    ]
+}

autobigs-cli.xml

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+<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@">0.4.2</token>
+		<token name="@VERSION_SUFFIX@">0</token>
+    	<import>autobigs-cli_macros.xml</import>
+	    <expand macro="bio_tools"/>
+	</macros>
+
+	<requirements>
+		<requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
+	</requirements>
+
+	<command detect_errors="exit_code"><![CDATA[
+			#if $operation == "info":
+				#if $retrieved == "schema":
+					autoBIGS info $selected_schema
+				#else if $retrieved == "databases":
+					autoBIGS info --retrieve-bigsdbs
+				#end if
+			#else if $operation == "st":
+				autoBIGS st $fastas $seqdefdb $schema $mlst_profiles_output
+			#end if
+	]]></command>
+	<inputs>
+		<conditional name="mode">
+			<param name="operation" label="Operation" type="select">
+				<option value="info"/>
+				<option value="st"/>
+			</param>
+			<when value="info">
+				<conditional name="select-info">
+					<param name="retrieved" label="Schema or Database List" type="select">
+						<option value="schema"/>
+						<option value="databases"/>
+					</param>
+					<when value="schema">
+						<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="integer" min="0"/>
+					</when>
+                    <when value="databases">
+                    <!-- No need to do anything -->
+                    </when>
+				</conditional>
+			</when>
+			<when value="st">
+				<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
+				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text"/>
+				<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
+			</when>
+		</conditional>
+	</inputs>
+	<outputs>
+		<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv" />
+	</outputs>
+    <tests>
+        <test>
+            <param name="operation" value="st" />
+            <param name="fastas" value="tohama_I_bpertussis.fasta" />
+            <param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
+            <param name="schema" value="3" />
+            <output name="mlst_profiles_output" file="results.csv" ftype="csv" />
+        </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
+  --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).
+
+
+	]]></help>
+    <citations>
+        <citation type="bibtex">
+@book{Deng2025RealYHD,
+title = {RealYHD/autoBIGS.cli},
+url = {https://github.com/RealYHD/autoBIGS.cli},
+author = {Deng, Harrison},
+date = {2025-01-24},
+year = {2025},
+month = {1},
+day = {24},
+}
+        </citation>
+    </citations>
+</tool>

autobigs-cli_macros.xml

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+<macros>
+  <xml name="bio_tools">
+    <xrefs>
+        <xref type="bio.tools">AutoBIGS.CLI</xref>
+    </xrefs>
+  </xml>
+</macros>

requirements.txt

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+planemo

test-data/results.csv

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