# HG changeset patch
# User iuc
# Date 1765575462 0
# Node ID 9e6d0309ec068ec34df86d0d5e517399d7fe48e5
# Parent  c80b2251cb78a6eace877cb68c902d0b2ec9a23e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit 31b55c90f2a622c8dceb93bb1142c46c43989d59

diff -r c80b2251cb78 -r 9e6d0309ec06 data_manager/data_manager_build_coreprofiler_download.xml
--- a/data_manager/data_manager_build_coreprofiler_download.xml	Mon Dec 08 11:36:13 2025 +0000
+++ b/data_manager/data_manager_build_coreprofiler_download.xml	Fri Dec 12 21:37:42 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="data_manager_build_coreprofiler" name="Download and build CoreProfiler scheme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@">
     <description></description>
     <macros>
-        <token name="@TOOL_VERSION@">1.1.8</token>
+        <token name="@TOOL_VERSION@">2.0.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@PROFILE@">22.05</token>
         <xml name="version_command">
@@ -27,21 +27,28 @@
         <requirement type="package" version="2.16.0">blast</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+#from datetime import date
+
 #set $scheme_name = str($select_db.coreprofiler_scheme_select).split('-')[0]
 #set $scheme_db = str($select_db.coreprofiler_scheme_select).split('-')[3]
+#set $today = date.today().strftime('%Y-%m-%d')
 
-#if hasattr($select_db, "db_version")
+#if $scheme_db == "pubmlst"
+    #set $db_version = str($select_db.db_version)
+#elif $scheme_db == "bigsdb"
     #set $db_version = str($select_db.db_version)
-#else
+#elif $scheme_db == "enterobase"
+    #set $db_version = "no_token"
+#elif $scheme_db == "cgmlstorg"
     #set $db_version = "no_token"
 #end if
 
 mkdir -p '$out_file.extra_files_path' &&
-mkdir -p coreprofiler_${scheme_name}_${db_version}/scheme_$scheme_name/ &&
-#if $db_version == "token_version"
+mkdir -p coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name/ &&
+#if $db_version == "token"
         #if $scheme_db == "pubmlst"
             source "$PUBMLST_COREPROFILER_SECRETS_PATH" &&
-        #elif $scheme_db == "BIGSdb"
+        #elif $scheme_db == "bigsdb"
             source "$BIGSDB_COREPROFILER_SECRETS_PATH" &&
         #end if
         if [[ -z "$COREPROFILER_CONSUMER_TOKEN" || -z "$COREPROFILER_CONSUMER_SECRET" || -z "$COREPROFILER_ACCESS_TOKEN" || -z "$COREPROFILER_ACCESS_SECRET" ]]; then
@@ -57,13 +64,13 @@
 
     coreprofiler db download 
         -s $scheme_name
-        -o coreprofiler_${scheme_name}_${db_version}/scheme_$scheme_name
+        -o coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name
         ## Used only for test 
         #if str($hide_test) == 'true':
             -t
         #end if
         ##
-#if $db_version == "token_version"
+#if $db_version == "token"
         -k "$COREPROFILER_CONSUMER_TOKEN"
         -ks "$COREPROFILER_CONSUMER_SECRET"
         -a "$COREPROFILER_ACCESS_TOKEN"
@@ -71,11 +78,11 @@
 #end if
 &&
 coreprofiler db makeblastdb
-    -s coreprofiler_${scheme_name}_${db_version}/scheme_$scheme_name 
+    -s coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name 
     -n $scheme_name 
-    -p coreprofiler_${scheme_name}_${db_version}/db_$scheme_name &&
+    -p coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_$scheme_name &&
 
-mv coreprofiler_${scheme_name}_${db_version} '$out_file.extra_files_path' &&
+mv coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today} '$out_file.extra_files_path' &&
 
 cp '$dmjson' '$out_file'
     ]]></command>
@@ -87,23 +94,39 @@
 #set $scheme_desc = str($select_db.coreprofiler_scheme_select).split('-')[1]
 #set $scheme_loci = str($select_db.coreprofiler_scheme_select).split('-')[2]
 #set $scheme_db = str($select_db.coreprofiler_scheme_select).split('-')[3]
-
+#set $today = date.today().strftime('%Y-%m-%d')
 
-#if hasattr($select_db, "db_version")
+#if $scheme_db == "pubmlst"
     #set $db_version = str($select_db.db_version)
-#else
+    #if $db_version == "no_token"
+        #set $db_date_version = "version before 2025"
+    #else
+        #set $db_date_version = "downloaded on " + $today
+    #end if
+#elif $scheme_db == "bigsdb"
+        #set $db_version = str($select_db.db_version)
+    #if $db_version == "no_token"
+        #set $db_date_version = "version before 2025"
+    #else
+        #set $db_date_version = "downloaded on " + $today
+    #end if
+#elif $scheme_db == "enterobase"
     #set $db_version = "no_token"
+    #set $db_date_version = "downloaded on " + $today
+#elif $scheme_db == "cgmlstorg"
+    #set $db_version = "no_token"
+    #set $db_date_version = "downloaded on " + $today
 #end if
 
 {
     "data_tables":{
     "coreprofiler_scheme":[
     {
-        "value": "coreprofiler_downloaded_#echo date.today().strftime('%d%m%Y')#-${scheme_name}-${scheme_desc}-${scheme_loci}-${scheme_db}-${db_version}",
-        "name": "${scheme_name}: ${scheme_desc} [${scheme_loci} loci] (${scheme_db}-${db_version})",
-        "path": "coreprofiler_${scheme_name}_${db_version}",
-        "database": "coreprofiler_${scheme_name}_${db_version}/db_${scheme_name}/${scheme_name}.fasta",
-        "scheme": "coreprofiler_${scheme_name}_${db_version}/scheme_${scheme_name}"
+        "value": "coreprofiler_downloaded_${today}-${scheme_name}-${scheme_desc}-${scheme_loci}-${scheme_db}-${db_version}",
+        "name": "${scheme_name}: ${scheme_desc} [${scheme_loci} loci] (${scheme_db} - ${db_date_version})",
+        "path": "coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}",
+        "database": "coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_${scheme_name}/${scheme_name}.fasta",
+        "scheme": "coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_${scheme_name}"
     }
     ]
 }
@@ -113,8 +136,9 @@
         <conditional name="select_db">
             <param name="db_list" type="select" label="Available database to download a schema">
                 <option value="pubmlst">pubMLST</option>
-                <option value="bigsdb">BigsDB</option>
+                <option value="bigsdb">BIGSdb</option>
                 <option value="enterobase">Enterobase</option>
+                <option value="cgmlstorg">cgMLST.org</option>
             </param>
             <when value="pubmlst">
                 <param name="db_version" type="select" label="Database version" >
@@ -123,6 +147,7 @@
                 </param>
                 <param name="coreprofiler_scheme_select" type="select" label="PubMLST schema supported by CoreProfiler">                   
                     <option value="abaumannii_3-cgMLST_v1-2133-pubmlst">abaumannii_3: cgMLST v1 [2133 loci] (pubmlst)</option>
+                    <option value="bcc_2-cgMLST-1925-pubmlst">bcc_2: cgMLST [1925 loci] (pubmlst)</option>
                     <option value="bcereus_2-B._anthracis_cgMLST-3803-pubmlst">bcereus_2: B. anthracis cgMLST [3803 loci] (pubmlst)</option>
                     <option value="bcereus_5-B._cereus_cgMLST-1568-pubmlst">bcereus_5: B. cereus cgMLST [1568 loci] (pubmlst)</option>
                     <option value="borrelia_3-cgMLST-639-pubmlst">borrelia_3: cgMLST [639 loci] (pubmlst)</option>
@@ -137,8 +162,10 @@
                     <option value="cperfringens_2-cgMLST-1431-pubmlst">cperfringens_2: cgMLST [1431 loci] (pubmlst)</option>
                     <option value="dnodosus_3-cgMLST-714-pubmlst">dnodosus_3: cgMLST [714 loci] (pubmlst)</option>
                     <option value="hinfluenzae_56-cgMLST_v1-1037-pubmlst">hinfluenzae_56: cgMLST v1 [1037 loci] (pubmlst)</option>
+                    <option value="hinfluenzae_59-H._parainfluenzae_cgMLST_v1-1062-pubmlst">hinfluenzae_59: H. parainfluenzae cgMLST v1 [1062 loci] (pubmlst)</option>
                     <option value="leptospira_4-cgMLST-1565-pubmlst">leptospira_4: cgMLST [1565 loci] (pubmlst)</option>
                     <option value="mabscessus_2-cgMLST-2904-pubmlst">mabscessus_2: cgMLST [2904 loci] (pubmlst)</option>
+                    <option value="mycobacteria_3-MTBC_cgMLST-1561-pubmlst">mycobacteria_3: MTBC cgMLST [1561 loci] (pubmlst)</option>
                     <option value="neisseria_72-Human_restricted_Neisseria_cgMLST-v1.0-1441-pubmlst">neisseria_72: Human-restricted Neisseria cgMLST v1.0 [1441 loci] (pubmlst)</option>
                     <option value="neisseria_45-L3_cgMLST-1742-pubmlst">neisseria_45: L3 cgMLST [1742 loci] (pubmlst)</option>
                     <option value="neisseria_68-L44_cgMLST-1699-pubmlst">neisseria_68: L44 cgMLST [1699 loci] (pubmlst)</option>
@@ -153,6 +180,7 @@
                     <option value="saureus_20-cgMLST-1716-pubmlst">saureus_20: cgMLST [1716 loci] (pubmlst)</option>
                     <option value="sagalactiae_38-h_S.agalactiae_cgMLST_v1.0-1405-pubmlst">sagalactiae_38: h_S.agalactiae cgMLST v1.0 [1405 loci] (pubmlst)</option>
                     <option value="spneumoniae_2-cgMLST-1222-pubmlst">spneumoniae_2: cgMLST [1222 loci] (pubmlst)</option>
+                    <option value="spyogenes_11-cgMLST-1198-pubmlst">spyogenes_11: cgMLST [1198 loci] (pubmlst)</option>
                     <option value="suberis_8-cgMLST-1447-pubmlst">suberis_8: cgMLST [1447 loci] (pubmlst)</option>
                     <option value="vcholerae_3-cgMLST-2443-pubmlst">vcholerae_3: cgMLST [2443 loci] (pubmlst)</option>
                     <option value="vparahaemolyticus_3-cgMLST-2254-pubmlst">vparahaemolyticus_3: cgMLST [2254 loci] (pubmlst)</option>
@@ -164,21 +192,25 @@
                     <option value="token" selected="true">Latest version (bash variables for tokens and secrets will have to be set as described in the documentation)</option>
                     <option value="no_token">Version before January 2025 (no tokens and secrets needed)</option>
                 </param>
-                <param name="coreprofiler_scheme_select" type="select" label="BigsDB schema supported by CoreProfiler">                   
-                    <option value="bordetella_1-cgMLST_genus-1415-BIGSdb">bordetella_1: cgMLST_genus [1415 loci] (BIGSdb)</option>
-                    <option value="bordetella_4-cgMLST_pertussis-2038-BIGSdb">bordetella_4: cgMLST_pertussis [2038 loci] (BIGSdb)</option>
-                    <option value="diphtheria_1-cgMLST-1305-BIGSdb">diphtheria_1: cgMLST [1305 loci] (BIGSdb)</option>
-                    <option value="diphtheria_5-cgMLST_ulcerans-1628-BIGSdb">diphtheria_5: cgMLST_ulcerans [1628 loci] (BIGSdb)</option>
-                    <option value="klebsiella_15-cgMLST_KpI-2537-BIGSdb">klebsiella_15: cgMLST_KpI [2537 loci] (BIGSdb)</option>
-                    <option value="klebsiella_10-cgMLST_ST258_ST512_ST1199-1371-BIGSdb">klebsiella_10: cgMLST_ST258_ST512_ST1199 [1371 loci] (BIGSdb)</option>
-                    <option value="klebsiella_18-scgMLST629_S-629-BIGSdb">klebsiella_18: scgMLST629_S [629 loci] (BIGSdb)</option>
-                    <option value="klebsiella_3-scgMLST634-632-BIGSdb">klebsiella_3: scgMLST634 [632 loci] (BIGSdb)</option>
-                    <option value="leptospira_3-capture_cgMLST-545-BIGSdb">leptospira_3: capture_cgMLST [545 loci] (BIGSdb)</option>
-                    <option value="leptospira_1-cgMLST-545-BIGSdb">leptospira_1: cgMLST [545 loci] (BIGSdb)</option>
-                    <option value="listeria_3-cgMLST1748-1748-BIGSdb">listeria_3: cgMLST1748 [1748 loci] (BIGSdb)</option>
-                    <option value="yersinia_2-Y.enterocolitica_cgMLST-1727-BIGSdb">yersinia_2: Y.enterocolitica cgMLST [1727 loci] (BIGSdb)</option>
-                    <option value="yersinia_1-Yersinia_cgMLST-500-BIGSdb">yersinia_1: Yersinia cgMLST [500 loci] (BIGSdb)</option>
-                    <option value="yersinia_3-Y.pseudotuberculosis_cgMLST-1921-BIGSdb">yersinia_3: Y.pseudotuberculosis cgMLST [1921 loci] (BIGSdb)</option>
+                <param name="coreprofiler_scheme_select" type="select" label="BIGSdb schema supported by CoreProfiler">                   
+                    <option value="bordetella_1-cgMLST_genus-1415-bigsdb">bordetella_1: cgMLST_genus [1415 loci] (bigsdb)</option>
+                    <option value="bordetella_4-cgMLST_pertussis-2038-bigsdb">bordetella_4: cgMLST_pertussis [2038 loci] (bigsdb)</option>
+                    <option value="diphtheria_1-cgMLST-1305-bigsdb">diphtheria_1: cgMLST [1305 loci] (bigsdb)</option>
+                    <option value="diphtheria_5-cgMLST_ulcerans-1628-bigsdb">diphtheria_5: cgMLST_ulcerans [1628 loci] (bigsdb)</option>
+                    <option value="klebsiella_15-cgMLST_KpI-2537-bigsdb">klebsiella_15: cgMLST_KpI [2537 loci] (bigsdb)</option>
+                    <option value="klebsiella_10-cgMLST_ST258_ST512_ST1199-1371-bigsdb">klebsiella_10: cgMLST_ST258_ST512_ST1199 [1371 loci] (bigsdb)</option>
+                    <option value="klebsiella_18-scgMLST629_S-629-bigsdb">klebsiella_18: scgMLST629_S [629 loci] (bigsdb)</option>
+                    <option value="klebsiella_19-Kpn_cgMLST-2752-bigsdb">klebsiella_19: Kpn_cgMLST [2752 loci] (BIGSdb)</option>
+                    <option value="klebsiella_26-SL147_cgMLST-852-bigsdb">klebsiella_26: SL147_cgMLST [852 loci] (BIGSdb)</option>
+                    <option value="klebsiella_27-cgMLST1748_v2-947-bigsdb">klebsiella_27: cgMLST1748_v2 [947 loci] (BIGSdb)</option>
+                    <option value="klebsiella_3-scgMLST634-632-bigsdb">klebsiella_3: scgMLST634 [632 loci] (bigsdb)</option>
+                    <option value="leptospira_3-capture_cgMLST-545-bigsdb">leptospira_3: capture_cgMLST [545 loci] (bigsdb)</option>
+                    <option value="leptospira_1-cgMLST-545-bigsdb">leptospira_1: cgMLST [545 loci] (bigsdb)</option>
+                    <option value="listeria_15-cgMLST-1748-bigsdb">listeria_15: cgMLST [1748 loci] (BIGSdb)</option>
+                    <option value="listeria_3-cgMLST1748-1748-bigsdb">listeria_3: cgMLST1748 [1748 loci] (bigsdb)</option>
+                    <option value="yersinia_2-Y.enterocolitica_cgMLST-1727-bigsdb">yersinia_2: Y.enterocolitica cgMLST [1727 loci] (bigsdb)</option>
+                    <option value="yersinia_1-Yersinia_cgMLST-500-bigsdb">yersinia_1: Yersinia cgMLST [500 loci] (bigsdb)</option>
+                    <option value="yersinia_3-Y.pseudotuberculosis_cgMLST-1921-bigsdb">yersinia_3: Y.pseudotuberculosis cgMLST [1921 loci] (bigsdb)</option>
                 </param>
             </when>
             <when value="enterobase">
@@ -187,6 +219,45 @@
                     <option value="salmonella_v2-cgMLST-3002-enterobase">salmonella_v2: cgMLST v2 [3002 loci] (enterobase)</option>
                 </param>
             </when>
+            <when value="cgmlstorg">
+                <param name="coreprofiler_scheme_select" type="select" label="cgMLST.org schema supported by CoreProfiler">                   
+                    <option value="abaumannii-Acinetobacter_baumannii-2390-cgmlstorg">abaumannii: Acinetobacter baumannii [2390 loci] (cgmlstorg)</option>
+                    <option value="banthracis-Bacillus_anthracis-3803-cgmlstorg">banthracis: Bacillus anthracis [3803 loci] (cgmlstorg)</option>
+                    <option value="bmallei_fli-Burkholderia_mallei_(FLI)-2838-cgmlstorg">bmallei_fli: Burkholderia mallei (FLI) [2838 loci] (cgmlstorg)</option>
+                    <option value="bmallei_rki-Burkholderia_mallei_(RKI)-3328-cgmlstorg">bmallei_rki: Burkholderia mallei (RKI) [3328 loci] (cgmlstorg)</option>
+                    <option value="bmelitensis-Brucella_melitensis-2704-cgmlstorg">bmelitensis: Brucella melitensis [2704 loci] (cgmlstorg)</option>
+                    <option value="bpertussis-Bordetella_pertussis-2983-cgmlstorg">bpertussis: Bordetella pertussis [2983 loci] (cgmlstorg)</option>
+                    <option value="bpseudomallei-Burkholderia_pseudomallei-4221-cgmlstorg">bpseudomallei: Burkholderia pseudomallei [4221 loci] (cgmlstorg)</option>
+                    <option value="cdifficile-Clostridioides_difficile-2147-cgmlstorg">cdifficile: Clostridioides difficile [2147 loci] (cgmlstorg)</option>
+                    <option value="cdiphtheriae-Corynebacterium_diphtheriae-1553-cgmlstorg">cdiphtheriae: Corynebacterium diphtheriae [1553 loci] (cgmlstorg)</option>
+                    <option value="cfreundii-Citrobacter_freundii-3250-cgmlstorg">cfreundii: Citrobacter freundii [3250 loci] (cgmlstorg)</option>
+                    <option value="cfreundii2-Citrobacter_freundii/portucalensis/braakii/europaeus-2307-cgmlstorg">cfreundii2: Citrobacter freundii/portucalensis/braakii/europaeus [2307 loci] (cgmlstorg)</option>
+                    <option value="cjejuni-Campylobacter_jejunicol-637-cgmlstorg">cjejuni: Campylobacter jejuni/coli [637 loci] (cgmlstorg)</option>
+                    <option value="cpseudotuberculosis-Corynebacterium_pseudotuberculosis-1577-cgmlstorg">cpseudotuberculosis: Corynebacterium pseudotuberculosis [1577 loci] (cgmlstorg)</option>
+                    <option value="csakazakii-Cronobacter_sakazakii/malonaticus-2831-cgmlstorg">csakazakii: Cronobacter sakazakii/malonaticus [2831 loci] (cgmlstorg)</option>
+                    <option value="efaecalis-Enterococcus_faecalis-1972-cgmlstorg">efaecalis: Enterococcus faecalis [1972 loci] (cgmlstorg)</option>
+                    <option value="efaecium-Enterococcus_faecium-1423-cgmlstorg">efaecium: Enterococcus faecium [1423 loci] (cgmlstorg)</option>
+                    <option value="ehormaechei-Enterobacter_hormaechei-2178-cgmlstorg">ehormaechei: Enterobacter hormaechei [2178 loci] (cgmlstorg)</option>
+                    <option value="ftularensis-Francisella_tularensis-1147-cgmlstorg">ftularensis: Francisella tularensis [1147 loci] (cgmlstorg)</option>
+                    <option value="koxytoca-Klebsiella_oxytoca/grimontii/michiganensis/pasteurii-2536-cgmlstorg">koxytoca: Klebsiella oxytoca/grimontii/michiganensis/pasteurii [2536 loci] (cgmlstorg)</option>
+                    <option value="kpneumoniae-Klebsiella_pneumoniae/variicola/quasipneumoniae-2358-cgmlstorg">kpneumoniae: Klebsiella pneumoniae/variicola/quasipneumoniae [2358 loci] (cgmlstorg)</option>
+                    <option value="lmonocytogenes-Listeria_monocytogenes-1701-cgmlstorg">lmonocytogenes: Listeria monocytogenes [1701 loci] (cgmlstorg)</option>
+                    <option value="lpneumophila-Legionella_pneumophila-1521-cgmlstorg">lpneumophila: Legionella pneumophila [1521 loci] (cgmlstorg)</option>
+                    <option value="mgallisepticum-Mycoplasma_gallisepticum-425-cgmlstorg">mgallisepticum: Mycoplasma gallisepticum [425 loci] (cgmlstorg)</option>
+                    <option value="mmorganii-Morganella_morganii-2462-cgmlstorg">mmorganii: Morganella morganii [2462 loci] (cgmlstorg)</option>
+                    <option value="mtuberculosis-Mycobacterium_tuberculosis/bovis/africanum/canettii-2891-cgmlstorg">mtuberculosis: Mycobacterium tuberculosis/bovis/africanum/canettii [2891 loci] (cgmlstorg)</option>
+                    <option value="paeruginosa-Pseudomonas_aeruginosa-3867-cgmlstorg">paeruginosa: Pseudomonas aeruginosa [3867 loci] (cgmlstorg)</option>
+                    <option value="plarvae-Paenibacillus_larvae-2419-cgmlstorg">plarvae: Paenibacillus larvae [2419 loci] (cgmlstorg)</option>
+                    <option value="pmirabilis-Proteus_mirabilis-2574-cgmlstorg">pmirabilis: Proteus mirabilis [2574 loci] (cgmlstorg)</option>
+                    <option value="pstuartii-Providencia_stuartii-3079-cgmlstorg">pstuartii: Providencia stuartii [3079 loci] (cgmlstorg)</option>
+                    <option value="sargenteus-Staphylococcus_argenteus-2168-cgmlstorg">sargenteus: Staphylococcus argenteus [2168 loci] (cgmlstorg)</option>
+                    <option value="saureus-Staphylococcus_aureus-1861-cgmlstorg">saureus: Staphylococcus aureus [1861 loci] (cgmlstorg)</option>
+                    <option value="scapitis-Staphylococcus_capitis-1492-cgmlstorg">scapitis: Staphylococcus capitis [1492 loci] (cgmlstorg)</option>
+                    <option value="smarcescens-Serratia_marcescens-2692-cgmlstorg">smarcescens: Serratia marcescens [2692 loci] (cgmlstorg)</option>
+                    <option value="spyogenes-Streptococcus_pyogenes-1095-cgmlstorg">spyogenes: Streptococcus pyogenes [1095 loci] (cgmlstorg)</option>
+                    <option value="yenterocolitica-Yersinia_enterocolitica-2582-cgmlstorg">yenterocolitica: Yersinia enterocolitica [2582 loci] (cgmlstorg)</option>
+                </param>
+            </when>
         </conditional>
         <!-- used only for tests, limit download scheme to 50 locus -->
         <param name="hide_test" type="hidden" value=""/>
@@ -206,11 +277,11 @@
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"coreprofiler_scheme":'/>
-                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-borrelia_3-cgMLST-639-pubmlst-no_token"'/>
-                    <has_text text='"name": "borrelia_3: cgMLST [639 loci] (pubmlst-no_token)"'/>
-                    <has_text text='"path": "coreprofiler_borrelia_3_no_token"'/>
-                    <has_text text='"database": "coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta"'/>
-                    <has_text text='"scheme": "coreprofiler_borrelia_3_no_token/scheme_borrelia_3"'/>
+                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-borrelia_3-cgMLST-639-pubmlst-no_token"'/>
+                    <has_text text='"name": "borrelia_3: cgMLST [639 loci] (pubmlst - version before 2025)"'/>
+                    <has_text_matching expression='"path": "coreprofiler_borrelia_3_pubmlst_no_token_[0-9-]{10}"'/>
+                    <has_text_matching expression='"database": "coreprofiler_borrelia_3_pubmlst_no_token_[0-9-]{10}/db_borrelia_3/borrelia_3.fasta"'/>
+                    <has_text_matching expression='"scheme": "coreprofiler_borrelia_3_pubmlst_no_token_[0-9-]{10}/scheme_borrelia_3"'/>
                 </assert_contents>
             </output>
         </test>
@@ -219,16 +290,16 @@
             <conditional name="select_db">
                 <param name="db_list" value="bigsdb"/>
                 <param name="db_version" value="no_token"/>
-                <param name="coreprofiler_scheme_select" value="yersinia_1-Yersinia_cgMLST-500-BIGSdb" />
+                <param name="coreprofiler_scheme_select" value="yersinia_1-Yersinia_cgMLST-500-bigsdb" />
             </conditional>
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"coreprofiler_scheme":'/>
-                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token"'/>
-                    <has_text text='"name": "yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)"'/>
-                    <has_text text='"path": "coreprofiler_yersinia_1_no_token"'/>
-                    <has_text text='"database": "coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta"'/>
-                    <has_text text='"scheme": "coreprofiler_yersinia_1_no_token/scheme_yersinia_1"'/>
+                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-yersinia_1-Yersinia_cgMLST-500-bigsdb-no_token"'/>
+                    <has_text text='"name": "yersinia_1: Yersinia_cgMLST [500 loci] (bigsdb - version before 2025)"'/>
+                    <has_text_matching expression='"path": "coreprofiler_yersinia_1_bigsdb_no_token_[0-9-]{10}"'/>
+                    <has_text_matching expression='"database": "coreprofiler_yersinia_1_bigsdb_no_token_[0-9-]{10}/db_yersinia_1/yersinia_1.fasta"'/>
+                    <has_text_matching expression='"scheme": "coreprofiler_yersinia_1_bigsdb_no_token_[0-9-]{10}/scheme_yersinia_1"'/>
                 </assert_contents>
             </output>
         </test>
@@ -241,11 +312,28 @@
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"coreprofiler_scheme":'/>
-                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9]{8}-escherichia_v1-cgMLST-2513-enterobase-no_token"'/>
-                    <has_text text='"name": "escherichia_v1: cgMLST [2513 loci] (enterobase-no_token)"'/>
-                    <has_text text='"path": "coreprofiler_escherichia_v1_no_token"'/>
-                    <has_text text='"database": "coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta"'/>
-                    <has_text text='"scheme": "coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1"'/>
+                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-escherichia_v1-cgMLST-2513-enterobase-no_token"'/>
+                    <has_text_matching expression='"name": "escherichia_v1: cgMLST \[2513 loci\] \(enterobase - downloaded on [0-9-]{10}\)"'/>
+                    <has_text_matching expression='"path": "coreprofiler_escherichia_v1_enterobase_no_token_[0-9-]{10}"'/>
+                    <has_text_matching expression='"database": "coreprofiler_escherichia_v1_enterobase_no_token_[0-9-]{10}/db_escherichia_v1/escherichia_v1.fasta"'/>
+                    <has_text_matching expression='"scheme": "coreprofiler_escherichia_v1_enterobase_no_token_[0-9-]{10}/scheme_escherichia_v1"'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="hide_test" value="true"/>
+            <conditional name="select_db">
+                <param name="db_list" value="cgmlstorg"/>
+                <param name="coreprofiler_scheme_select" value="mgallisepticum-Mycoplasma_gallisepticum-425-cgmlstorg" />
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text='"coreprofiler_scheme":'/>
+                    <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-mgallisepticum-Mycoplasma_gallisepticum-425-cgmlstorg-no_token"'/>
+                    <has_text_matching expression='"name": "mgallisepticum: Mycoplasma_gallisepticum \[425 loci\] \(cgmlstorg - downloaded on [0-9-]{10}\)"'/>
+                    <has_text_matching expression='"path": "coreprofiler_mgallisepticum_cgmlstorg_no_token_[0-9-]{10}"'/>
+                    <has_text_matching expression='"database": "coreprofiler_mgallisepticum_cgmlstorg_no_token_[0-9-]{10}/db_mgallisepticum/mgallisepticum.fasta"'/>
+                    <has_text_matching expression='"scheme": "coreprofiler_mgallisepticum_cgmlstorg_no_token_[0-9-]{10}/scheme_mgallisepticum"'/>
                 </assert_contents>
             </output>
         </test>
@@ -261,6 +349,7 @@
 - **pubMLST**
 - **BIGSdb**
 - **EnteroBase**
+- **cgMLST.org**
 
 The list of available schemes is maintained in the `CoreProfiler documentation <https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md#basic-usage>`_.
 
@@ -281,6 +370,7 @@
 Authentication is **not needed** for:
 
 - **EnteroBase**
+- **cgMLST.org**
 
 
 Authentication **is recommended** for:
@@ -358,4 +448,4 @@
     <citations>
         <citation type="doi">10.3390/microorganisms10020292</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file
diff -r c80b2251cb78 -r 9e6d0309ec06 test-data/coreprofiler_scheme.loc.test
--- a/test-data/coreprofiler_scheme.loc.test	Mon Dec 08 11:36:13 2025 +0000
+++ b/test-data/coreprofiler_scheme.loc.test	Fri Dec 12 21:37:42 2025 +0000
@@ -7,19 +7,4 @@
 #value	name	path	database	scheme
 #
 #For example
-#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	coreprofiler_klebsiella_3	coreprofiler_klebsiella_3/db_klebsiella_3/klebsiella_3.fasta	coreprofiler_klebsiella_3/scheme_klebsiella_3
-coreprofiler_downloaded_10102025-borrelia_3-cgMLST-639-pubmlst-no_token	borrelia_3: cgMLST [639 loci] (pubmlst-no_token)	/tmp/tmphn3k3ekk/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token	coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta	coreprofiler_borrelia_3_no_token/scheme_borrelia_3
-coreprofiler_downloaded_10102025-bordetella_1-cgMLST_genus-1415-BIGSdb-no_token	bordetella_1: cgMLST_genus [1415 loci] (BIGSdb-no_token)	/tmp/tmphn3k3ekk/galaxy-dev/tool-data/coreprofiler/coreprofiler_bordetella_1_no_token	coreprofiler_bordetella_1_no_token/db_bordetella_1/bordetella_1.fasta	coreprofiler_bordetella_1_no_token/scheme_bordetella_1
-coreprofiler_downloaded_28102025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token	yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)	/tmp/tmpomzcgw6j/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token	coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta	coreprofiler_yersinia_1_no_token/scheme_yersinia_1
-coreprofiler_downloaded_17112025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token	yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)	/tmp/tmphe1udqum/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token	coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta	coreprofiler_yersinia_1_no_token/scheme_yersinia_1
-coreprofiler_downloaded_17112025-escherichia_v1-cgMLST-2513-enterobase-no_token	escherichia_v1: cgMLST [2513 loci] (enterobase-no_token)	/tmp/tmphe1udqum/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token	coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta	coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1
-coreprofiler_downloaded_17112025-borrelia_3-cgMLST-639-pubmlst-no_token	borrelia_3: cgMLST [639 loci] (pubmlst-no_token)	/tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token	coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta	coreprofiler_borrelia_3_no_token/scheme_borrelia_3
-coreprofiler_downloaded_17112025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token	yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)	/tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token	coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta	coreprofiler_yersinia_1_no_token/scheme_yersinia_1
-coreprofiler_downloaded_17112025-escherichia_v1-cgMLST-2513-enterobase-no_token	escherichia_v1: cgMLST [2513 loci] (enterobase-no_token)	/tmp/tmp6njg6emw/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token	coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta	coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1
-coreprofiler_downloaded_03122025-borrelia_3-cgMLST-639-pubmlst-no_token	borrelia_3: cgMLST [639 loci] (pubmlst-no_token)	/tmp/tmpjqeo859k/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token	coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta	coreprofiler_borrelia_3_no_token/scheme_borrelia_3
-coreprofiler_downloaded_03122025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token	yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)	/tmp/tmpjqeo859k/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token	coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta	coreprofiler_yersinia_1_no_token/scheme_yersinia_1
-coreprofiler_downloaded_03122025-escherichia_v1-cgMLST-2513-enterobase-no_token	escherichia_v1: cgMLST [2513 loci] (enterobase-no_token)	/tmp/tmpjqeo859k/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token	coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta	coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1
-coreprofiler_downloaded_03122025-mgallisepticum1387-Mycoplasma_gallisepticum-425-cgmlstorg-no_token	mgallisepticum1387: Mycoplasma_gallisepticum [425 loci] (cgmlstorg-no_token)	/tmp/tmpjqeo859k/galaxy-dev/tool-data/coreprofiler/coreprofiler_mgallisepticum1387_no_token	coreprofiler_mgallisepticum1387_no_token/db_mgallisepticum1387/mgallisepticum1387.fasta	coreprofiler_mgallisepticum1387_no_token/scheme_mgallisepticum1387
-coreprofiler_downloaded_08122025-borrelia_3-cgMLST-639-pubmlst-no_token	borrelia_3: cgMLST [639 loci] (pubmlst-no_token)	/tmp/tmpxd63w063/galaxy-dev/tool-data/coreprofiler/coreprofiler_borrelia_3_no_token	coreprofiler_borrelia_3_no_token/db_borrelia_3/borrelia_3.fasta	coreprofiler_borrelia_3_no_token/scheme_borrelia_3
-coreprofiler_downloaded_08122025-yersinia_1-Yersinia_cgMLST-500-BIGSdb-no_token	yersinia_1: Yersinia_cgMLST [500 loci] (BIGSdb-no_token)	/tmp/tmpxd63w063/galaxy-dev/tool-data/coreprofiler/coreprofiler_yersinia_1_no_token	coreprofiler_yersinia_1_no_token/db_yersinia_1/yersinia_1.fasta	coreprofiler_yersinia_1_no_token/scheme_yersinia_1
-coreprofiler_downloaded_08122025-escherichia_v1-cgMLST-2513-enterobase-no_token	escherichia_v1: cgMLST [2513 loci] (enterobase-no_token)	/tmp/tmpxd63w063/galaxy-dev/tool-data/coreprofiler/coreprofiler_escherichia_v1_no_token	coreprofiler_escherichia_v1_no_token/db_escherichia_v1/escherichia_v1.fasta	coreprofiler_escherichia_v1_no_token/scheme_escherichia_v1
+#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	coreprofiler_klebsiella_3	coreprofiler_klebsiella_3/db_klebsiella_3/klebsiella_3.fasta	coreprofiler_klebsiella_3/scheme_klebsiella_3
\ No newline at end of file