.gitignore

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

.vscode/extensions.json

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

.vscode/tasks.json

@@ -8,18 +8,6 @@
             "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

@@ -1,33 +0,0 @@
-pipeline {
-    agent {
-        kubernetes {
-            cloud 'rsys-devel'
-            defaultContainer 'pip'
-            inheritFrom 'pip'
-        }
-    }
-    
-    stages {
-        stage ("install") {
-            steps {
-                sh 'useradd galaxy -m'
-                sh 'apt update'
-                sh 'apt install sudo -y'
-                sh 'pip install -r requirements.txt'
-                sh 'pip install standard-imghdr'
-            }
-        }
-        stage ("lint") {
-            steps {
-                sh "planemo lint autobigs-cli.xml"
-            }
-        }
-        stage ("test") {
-            steps {
-                sh '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)]
-            }
-        }
-    }
-}

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@">0.5.0</token>
+		<token name="@TOOL_VERSION@">0.4.3</token>
 		<token name="@VERSION_SUFFIX@">0</token>
     	<import>autobigs-cli_macros.xml</import>
 	    <expand macro="bio_tools"/>
@@ -12,74 +12,57 @@
 	</requirements>
 
 	<command detect_errors="exit_code"><![CDATA[
-			#if $mode['operation'] == "info":
+			#if $operation == "info":
-				#if $select_info['retrieved'] == "schemas":
+				#if $retrieved == "schema":
-					autoBIGS info $selected_schema --csv $info_db_out
+					autoBIGS info $selected_schema
-				#else if $select_info['retrieved'] == "databases":
+				#else if $retrieved == "databases":
-					autoBIGS info --retrieve-bigsdbs --csv $info_schemes_out
+					autoBIGS info --retrieve-bigsdbs
 				#end if
-			#else if $mode['operation'] == "st":
+			#else if $operation == "st":
-				autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
+				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">Retrieve Database Information</option>
+				<option value="info"/>
-				<option value="st">Perform Sequence Typing</option>
+				<option value="st"/>
 			</param>
 			<when value="info">
-				<conditional name="select_info">
+				<conditional name="select-info">
-					<param name="retrieved" label="Schemas or Database List" type="select">
+					<param name="retrieved" label="Schema or Database List" type="select">
-						<option value="schemes">Available Schemas for Database</option>
+						<option value="schema"/>
-						<option value="databases">Available Databases</option>
+						<option value="databases"/>
 					</param>
-					<when value="schemes">
+					<when value="schema">
-						<repeat name="schemes_list" title="Schemes" min="1">
+						<repeat name="schemas" title="Schemas">
-							<param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
+							<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" optional="false"/>
+				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text"/>
 				<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 ${on_string}" format="csv">
-			<filter>mode['operation'] == "st"</filter>
+			<filter>mode == "st"</filter>
-		</data>
-		<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
-			<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter>
-		</data>
-		<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
-			<filter>mode['operation'] == "info" and select_info['retrieved'] == 'schemes'</filter>
 		</data>
 	</outputs>
     <tests>
-        <test expect_num_outputs="1">
+        <test>
             <param name="operation" value="st" />
-            <param name="fastas" value="tohama_I_bpertussis_wgs.fasta" />
+            <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="tohama_I_bpertussis_wgs_typed.csv" ftype="csv" />
+            <output name="mlst_profiles_output" file="results.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[
@@ -106,6 +89,7 @@ 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).
 
@@ -114,8 +98,8 @@ options:
     <citations>
         <citation type="bibtex">
 @book{Deng2025RealYHD,
-title = {Syph-and-VPD-Lab/autoBIGS.cli},
+title = {RealYHD/autoBIGS.cli},
-url = {https://github.com/Syph-and-VPD-Lab/autoBIGS.cli},
+url = {https://github.com/RealYHD/autoBIGS.cli},
 author = {Deng, Harrison},
 date = {2025-01-24},
 year = {2025},

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

@@ -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

test-data/results.csv

@@ -0,0 +1,2 @@
+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

@@ -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

test-data/tohama_I_bpertussis_wgs_typed.csv

@@ -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