Added Galaxy repo as a submodule

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

@@ -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": {},

.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 +1,3 @@
-autobigs-cli_test_report.html
 galaxy-server/**
+test_results
+autobigs-cli_test_report.html

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "auto-updated-tools-iuc"]
+	path = auto-updated-tools-iuc
+	url = https://github.com/Syph-and-VPD-Lab/auto-updated-tools-iuc.git
+[submodule "galaxy"]
+	path = galaxy
+	url = https://github.com/galaxyproject/galaxy.git

.vscode/extensions.json

@@ -1,8 +1,8 @@
 {
     "recommendations": [
-        "davelopez.galaxy-tools",
         "mechatroner.rainbow-csv",
         "redhat.vscode-xml",
-        "ms-vscode.live-server"
+        "ms-vscode.live-server",
+        "davelopez.galaxy-tools"
     ]
 }

.vscode/tasks.json

@@ -6,7 +6,19 @@
         {
             "label": "lint",
             "type": "shell",
-            "command": "planemo lint",
+            "command": "planemo lint auto-updated-tools-iuc/tools/autobigs",
+            "problemMatcher": []
+        },
+        {
+            "label": "serve",
+            "type": "shell",
+            "command": "planemo serve auto-updated-tools-iuc/tools/autobigs --conda_channels https://git.reslate.systems/api/packages/ydeng/conda,bioconda,conda-forge",
+            "problemMatcher": []
+        },
+        {
+            "label": "run tests",
+            "type": "shell",
+            "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",
             "problemMatcher": []
         }
     ]

Jenkinsfile

@@ -0,0 +1,31 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
+        }
+    }
+    
+    stages {
+        stage ("install") {
+            steps {
+                sh 'pip install -r requirements.txt'
+                sh 'pip install standard-imghdr'
+                sh 'planemo ci_setup'
+            }
+        }
+        stage ("lint") {
+            steps {
+                sh "planemo lint autobigs-cli.xml"
+            }
+        }
+        stage ("test") {
+            steps {
+                sh 'mkdir test_results'
+                sh "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

@@ -1,111 +0,0 @@
-<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="@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 $mlst_profiles_output
-			#end if
-	]]></command>
-	<inputs>
-		<conditional name="mode">
-			<param name="operation" label="Operation" type="select">
-				<option value="info"/>
-				<option value="st"/>
-			</param>
-			<when value="info">
-				<conditional name="select-info">
-					<param name="retrieved" label="Schema or Database List" type="select">
-						<option value="schema"/>
-						<option value="databases"/>
-					</param>
-					<when value="schema">
-						<repeat name="schemas" title="Schemas">
-							<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="integer" min="0"/>
-						</repeat>
-					</when>
-                    <when value="databases">
-                    <!-- No need to do anything -->
-                    </when>
-				</conditional>
-			</when>
-			<when value="st">
-				<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
-				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text"/>
-				<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
-			</when>
-		</conditional>
-	</inputs>
-	<outputs>
-		<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
-			<filter>mode == "st"</filter>
-		</data>
-	</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

@@ -1,7 +0,0 @@
-<macros>
-  <xml name="bio_tools">
-    <xrefs>
-        <xref type="bio.tools">AutoBIGS.CLI</xref>
-    </xrefs>
-  </xml>
-</macros>

environment.yml

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

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