Mercurial > repos > iuc > data_manager_build_coreprofiler

changeset 2:c80b2251cb78 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit d62ee14bc52c85cc771db52d34fac796e660f848
author iuc
date Mon, 08 Dec 2025 11:36:13 +0000
parents a95177c4d627
children 9e6d0309ec06
files data_manager/data_manager_build_coreprofiler_download.xml test-data/coreprofiler_scheme.loc.test
diffstat 2 files changed, 196 insertions(+), 124 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_build_coreprofiler_download.xml	Fri Nov 21 13:12:00 2025 +0000
+++ b/data_manager/data_manager_build_coreprofiler_download.xml	Mon Dec 08 11:36:13 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@">1.1.7</token>
+        <token name="@TOOL_VERSION@">1.1.8</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@PROFILE@">22.05</token>
         <xml name="version_command">
@@ -27,15 +27,23 @@
         <requirement type="package" version="2.16.0">blast</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#set $scheme_name = str($coreprofiler_scheme_select).split('-')[0]
-#set $scheme_db = str($coreprofiler_scheme_select).split('-')[3]
+#set $scheme_name = str($select_db.coreprofiler_scheme_select).split('-')[0]
+#set $scheme_db = str($select_db.coreprofiler_scheme_select).split('-')[3]
 
-#set $db_version = str($db_version)
+#if hasattr($select_db, "db_version")
+    #set $db_version = str($select_db.db_version)
+#else
+    #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 $db_version == "token_version"
-        source "$COREPROFILER_SECRETS_PATH" &&
+        #if $scheme_db == "pubmlst"
+            source "$PUBMLST_COREPROFILER_SECRETS_PATH" &&
+        #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
             echo "Error: Missing required bash variables for CoreProfiler authentication." >&2
             echo "Please set the following variables before running this tool:" >&2
@@ -75,12 +83,17 @@
         <configfile name="dmjson"><![CDATA[
 #from datetime import date
 
-#set $scheme_name = str($coreprofiler_scheme_select).split('-')[0]
-#set $scheme_desc = str($coreprofiler_scheme_select).split('-')[1]
-#set $scheme_loci = str($coreprofiler_scheme_select).split('-')[2]
-#set $scheme_db = str($coreprofiler_scheme_select).split('-')[3]
+#set $scheme_name = str($select_db.coreprofiler_scheme_select).split('-')[0]
+#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 $db_version = str($db_version)
+#if hasattr($select_db, "db_version")
+    #set $db_version = str($select_db.db_version)
+#else
+    #set $db_version = "no_token"
+#end if
 
 {
     "data_tables":{
@@ -97,66 +110,87 @@
         }]]></configfile>
     </configfiles>
     <inputs>
-            <param name="db_version" type="select" label="Select if you want latest version from pubMLST or BigsDB using tokens" help="If you choose latest, you will have to provide tokens and secrets to access the database following the procedure describe in the documentation." >
-                <option value="token" selected="true">Latest version from pubMLST or BigsDB, you will need to set bash variables for tokens and secrets as described in the documentation.</option>
-                <option value="no_token">No need of tokens but it will download the previous version, not the latest version, from pubMLST or BigsDB or if you want a database from Enterobase</option>
+        <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="enterobase">Enterobase</option>
             </param>
+            <when value="pubmlst">
+                <param name="db_version" type="select" label="Database version" >
+                    <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="PubMLST schema supported by CoreProfiler">                   
+                    <option value="abaumannii_3-cgMLST_v1-2133-pubmlst">abaumannii_3: cgMLST v1 [2133 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>
+                    <option value="brucella_3-cgMLST-1764-pubmlst">brucella_3: cgMLST [1764 loci] (pubmlst)</option>
+                    <option value="bmallei_1-cgMLST-3311-pubmlst">bmallei_1: cgMLST [3311 loci] (pubmlst)</option>
+                    <option value="bpseudomallei_2-cgMLST-4090-pubmlst">bpseudomallei_2: cgMLST [4090 loci] (pubmlst)</option>
+                    <option value="campylobacter_4-C._jejuni_/_C._coli_cgMLST_v1-1343-pubmlst">campylobacter_4: C. jejuni / C. coli cgMLST v1 [1343 loci] (pubmlst)</option>
+                    <option value="campylobacter_8-C._jejuni_/_C._coli_cgMLST_v2-1142-pubmlst">campylobacter_8: C. jejuni / C. coli cgMLST v2 [1142 loci] (pubmlst)</option>
+                    <option value="chlamydiales_44-C._abortus_cgMLST_v1.0-959-pubmlst">chlamydiales_44: C. abortus cgMLST v1.0 [959 loci] (pubmlst)</option>
+                    <option value="chlamydiales_42-C._trachomatis_cgMLST_v1.0-817-pubmlst">chlamydiales_42: C. trachomatis cgMLST v1.0 [817 loci] (pubmlst)</option>
+                    <option value="cchauvoei_1-cgMLST-2223-pubmlst">cchauvoei_1: cgMLST [2223 loci] (pubmlst)</option>
+                    <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="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="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>
+                    <option value="neisseria_62-N._gonorrhoeae_cgMLST_v1.0-1649-pubmlst">neisseria_62: N. gonorrhoeae cgMLST v1.0 [1649 loci] (pubmlst)</option>
+                    <option value="neisseria_89-N._gonorrhoeae_cgMLST_v2-1430-pubmlst">neisseria_89: N. gonorrhoeae cgMLST v2 [1430 loci] (pubmlst)</option>
+                    <option value="neisseria_47-N._meningitidis_cgMLST_v1-1605-pubmlst">neisseria_47: N. meningitidis cgMLST v1 [1605 loci] (pubmlst)</option>
+                    <option value="neisseria_85-N._meningitidis_cgMLST_v2-1422-pubmlst">neisseria_85: N. meningitidis cgMLST v2 [1422 loci] (pubmlst)</option>
+                    <option value="neisseria_88-N._meningitidis_cgMLST_v3-1329-pubmlst">neisseria_88: N. meningitidis cgMLST v3 [1329 loci] (pubmlst)</option>
+                    <option value="pmultocida_3-cgMLST_draft_1233-pubmlst">pmultocida_3: cgMLST (draft) [1233 loci] (pubmlst)</option>
+                    <option value="salmonella_3-SalmcgMLST_v1.0-2750-pubmlst">salmonella_3: SalmcgMLST v1.0 [2750 loci] (pubmlst)</option>
+                    <option value="serratia_2-cgMLST-2692-pubmlst">serratia_2: cgMLST [2692 loci] (pubmlst)</option>
+                    <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="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>
+                    <option value="xcitri_1-cgMLST-1618-pubmlst">xcitri_1: cgMLST [1618 loci] (pubmlst)</option>
+                </param>
+            </when>
+            <when value="bigsdb">
+                <param name="db_version" type="select" label="Database version" >
+                    <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>
+            </when>
+            <when value="enterobase">
+                <param name="coreprofiler_scheme_select" type="select" label="Enterobase schema supported by CoreProfiler">                   
+                    <option value="escherichia_v1-cgMLST-2513-enterobase">escherichia_v1: cgMLST v1 [2513 loci] (enterobase)</option>
+                    <option value="salmonella_v2-cgMLST-3002-enterobase">salmonella_v2: cgMLST v2 [3002 loci] (enterobase)</option>
+                </param>
+            </when>
+        </conditional>
         <!-- used only for tests, limit download scheme to 50 locus -->
         <param name="hide_test" type="hidden" value=""/>
         <!-- -->
-        <param name="coreprofiler_scheme_select" type="select" label="CoreProfiler available scheme" help="Choose a schema from a reference platform supported in 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>
-            <option value="abaumannii_3-cgMLST_v1-2133-pubmlst">abaumannii_3: cgMLST v1 [2133 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>
-            <option value="brucella_3-cgMLST-1764-pubmlst">brucella_3: cgMLST [1764 loci] (pubmlst)</option>
-            <option value="bmallei_1-cgMLST-3311-pubmlst">bmallei_1: cgMLST [3311 loci] (pubmlst)</option>
-            <option value="bpseudomallei_2-cgMLST-4090-pubmlst">bpseudomallei_2: cgMLST [4090 loci] (pubmlst)</option>
-            <option value="campylobacter_4-C._jejuni_/_C._coli_cgMLST_v1-1343-pubmlst">campylobacter_4: C. jejuni / C. coli cgMLST v1 [1343 loci] (pubmlst)</option>
-            <option value="campylobacter_8-C._jejuni_/_C._coli_cgMLST_v2-1142-pubmlst">campylobacter_8: C. jejuni / C. coli cgMLST v2 [1142 loci] (pubmlst)</option>
-            <option value="chlamydiales_44-C._abortus_cgMLST_v1.0-959-pubmlst">chlamydiales_44: C. abortus cgMLST v1.0 [959 loci] (pubmlst)</option>
-            <option value="chlamydiales_42-C._trachomatis_cgMLST_v1.0-817-pubmlst">chlamydiales_42: C. trachomatis cgMLST v1.0 [817 loci] (pubmlst)</option>
-            <option value="cchauvoei_1-cgMLST-2223-pubmlst">cchauvoei_1: cgMLST [2223 loci] (pubmlst)</option>
-            <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="escherichia_v1-cgMLST-2513-enterobase">escherichia_v1: cgMLST v1 [2513 loci] (enterobase)</option>
-            <option value="hinfluenzae_56-cgMLST_v1-1037-pubmlst">hinfluenzae_56: cgMLST v1 [1037 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="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>
-            <option value="neisseria_62-N._gonorrhoeae_cgMLST_v1.0-1649-pubmlst">neisseria_62: N. gonorrhoeae cgMLST v1.0 [1649 loci] (pubmlst)</option>
-            <option value="neisseria_89-N._gonorrhoeae_cgMLST_v2-1430-pubmlst">neisseria_89: N. gonorrhoeae cgMLST v2 [1430 loci] (pubmlst)</option>
-            <option value="neisseria_47-N._meningitidis_cgMLST_v1-1605-pubmlst">neisseria_47: N. meningitidis cgMLST v1 [1605 loci] (pubmlst)</option>
-            <option value="neisseria_85-N._meningitidis_cgMLST_v2-1422-pubmlst">neisseria_85: N. meningitidis cgMLST v2 [1422 loci] (pubmlst)</option>
-            <option value="neisseria_88-N._meningitidis_cgMLST_v3-1329-pubmlst">neisseria_88: N. meningitidis cgMLST v3 [1329 loci] (pubmlst)</option>
-            <option value="pmultocida_3-cgMLST_draft_1233-pubmlst">pmultocida_3: cgMLST (draft) [1233 loci] (pubmlst)</option>
-            <option value="salmonella_v2-cgMLST-3002-enterobase">salmonella_v2: cgMLST v2 [3002 loci] (enterobase)</option>
-            <option value="salmonella_3-SalmcgMLST_v1.0-2750-pubmlst">salmonella_3: SalmcgMLST v1.0 [2750 loci] (pubmlst)</option>
-            <option value="serratia_2-cgMLST-2692-pubmlst">serratia_2: cgMLST [2692 loci] (pubmlst)</option>
-            <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="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>
-            <option value="xcitri_1-cgMLST-1618-pubmlst">xcitri_1: cgMLST [1618 loci] (pubmlst)</option>
-        </param>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" label="${tool.name}"/>
@@ -164,8 +198,11 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="hide_test" value="true"/>
-            <param name="coreprofiler_scheme_select" value="borrelia_3-cgMLST-639-pubmlst" />
-            <param name="db_version" value="no_token"/>
+            <conditional name="select_db">
+                <param name="db_list" value="pubmlst"/>
+                <param name="db_version" value="no_token"/>
+                <param name="coreprofiler_scheme_select" value="borrelia_3-cgMLST-639-pubmlst" />
+            </conditional>
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"coreprofiler_scheme":'/>
@@ -179,8 +216,11 @@
         </test>
         <test expect_num_outputs="1">
             <param name="hide_test" value="true"/>
-            <param name="coreprofiler_scheme_select" value="yersinia_1-Yersinia_cgMLST-500-BIGSdb" />
-            <param name="db_version" value="no_token"/>
+            <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" />
+            </conditional>
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"coreprofiler_scheme":'/>
@@ -194,8 +234,10 @@
         </test>
         <test expect_num_outputs="1">
             <param name="hide_test" value="true"/>
-            <param name="coreprofiler_scheme_select" value="escherichia_v1-cgMLST-2513-enterobase" />
-            <param name="db_version" value="no_token"/>
+            <conditional name="select_db">
+                <param name="db_list" value="enterobase"/>
+                <param name="coreprofiler_scheme_select" value="escherichia_v1-cgMLST-2513-enterobase" />
+            </conditional>
             <output name="out_file">
                 <assert_contents>
                     <has_text text='"coreprofiler_scheme":'/>
@@ -209,20 +251,50 @@
         </test>
     </tests>
     <help><![CDATA[
-This tool downloads and builds the **CoreProfiler** scheme.
+This tool downloads and installs **CoreProfiler** schemes into Galaxy using the Data Manager framework.
+
+Overview
+--------
 
-You can find the list of available scheme, as well as the reference platforms supported by CoreProfiler, in the <a href="https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md?ref_type=heads#basic-usage" target="_blank">CoreProfiler documentation</a>.
+CoreProfiler supports several reference platforms:
+
+- **pubMLST**
+- **BIGSdb**
+- **EnteroBase**
+
+The list of available schemes is maintained in the `CoreProfiler documentation <https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md#basic-usage>`_.
 
 Please refer to this page for details on how to use the tool and which schema options are available.
 
-Use Galaxy's data manager framework to download and install new CoreProfiler schemes :
+You simply need to choose:
+1. A reference platform  
+2. A scheme available on that platform  
+3. Whether authentication is required (pubMLST / BIGSdb only)
+
+Galaxy will download the database, build the scheme, and register it automatically.
 
-If you want to use a scheme from enterobase, you do not need to provide any token or secret.
+---
+
+Authentication requirements
+---------------------------
+
+Authentication is **not needed** for:
 
-However, if you want to use a scheme from **pubMLST** or **BigsDB**, you will need to follow a procedure before launching the data manager.
+- **EnteroBase**
+
+
+Authentication **is recommended** for:
+
+- **pubMLST**
+- **BIGSdb**
 
-BIGSdb and PubMLST platforms require OAuth1 authentication to access and download the most up-to-date schemes.
-While authentication is not strictly mandatory, skipping it may result in downloading outdated schemes.
+
+Why?
+````
+
+BIGSdb and pubMLST platforms require **OAuth1** authentication and restrict access to the most up-to-date data.  
+While authentication is not strictly mandatory, skipping it may result in downloading **outdated** schemes.
+
 
 This authentication involves two types of tokens:
 
@@ -230,66 +302,59 @@
 
  * Access tokens : tokens required to download a scheme.
 
-Procedure for pubMLST schemes (example with borrelia_3-cgMLST-639-pubmlst) :
+---
 
-1. Create an account on the <a href="https://pubmlst.org/bigsdb" target="_blank">pubMLST</a> website.
-2. Generate a consumer token and secret from your account settings (My account > API keys > Enter key name > Submit).
-3. On your account page, go to Database registrations, check all databases and register.
-4. Download <a href="https://gitlab.com/ifb-elixirfr/abromics/coreprofiler" target="_blank">coreprofiler</a> locally and run the following command to obtain your access token and secret
+Procedure to obtain pubMLST and BIGSdb schemes
+----------------------------------------------
 
-Replace the placeholders with your scheme of interest (example : borrelia_3) your actual consumer token and secret :
-
-"""
-coreprofiler db get_request_tokens --scheme <SCHEME_NAME> --consumer_key <YOUR_CONSUMER_TOKEN> --consumer_secret <YOUR_CONSUMER_SECRET>
-"""
-
-This command will provide you with a URL to visit in order to authorize client software to access your account. 
+Example
+```````
+- **pubMLST**: borrelia_3-cgMLST-639-pubmlst
+- **BIGSdb**: bordetella_1-cgMLST_genus-1415-BIGSdb
 
-After authorizing, it will give you a verification code that you need to enter in the command line prompt.
-
-It will then return your access token and secret.
-
-5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool by setting this bash variables in a txt file : 
+1. Create an account on the `pubMLST <https://pubmlst.org/bigsdb>`_ or `BigsDB <https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?page=registration>`_ website.
+2. Generate a **consumer token** and **consumer secret** 
+   * **pubMLST**: From your account settings (My account > API keys > Enter key name > Submit).
+   * **BIGSdb**: By sending a mail to bigsdb@pasteur.fr (object "API client key").
+3. On your account page, go to **Database registrations**, check all databases and register.
+4. Download and install `coreprofiler <https://gitlab.com/ifb-elixirfr/abromics/coreprofiler>`_ locally and run the following command to **obtain your access token and secret**
 
-"""
-export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>"
-export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>"
-export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>"
-export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>"
-"""
+Replace the placeholders with your scheme of interest (example : *borrelia_3* or *bordetella_1*) your actual consumer token and secret :
 
-6. Set the path to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt").
+::
+
+    coreprofiler db get_request_tokens --scheme <SCHEME_NAME> --consumer_key <YOUR_CONSUMER_TOKEN> --consumer_secret <YOUR_CONSUMER_SECRET>
+
 
-Procedure for BigsDB (example with bordetella_1-cgMLST_genus-1415-BIGSdb):
+This command will provide you with a URL to visit in order to **authorize client software** to access your account. 
+After authorizing, it will give you a **verification code** that you need to enter in the command line prompt.
+It will then return **your access token and secret**.
 
-1. Create an account on the <a href="https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?page=registration" target="_blank">BigsDB</a> website.
-2. Ask for a consumer token and secret by sending a mail to bigsdb@pasteur.fr (object "API client key").
-3. On your account page, go to Database registrations, check all databases and register.
-4. Download <a href="https://gitlab.com/ifb-elixirfr/abromics/coreprofiler" target="_blank">coreprofiler</a> locally and run the following command to obtain your access token and secret
+5. Provide the **consumer token**, **consumer secret**, **access token**, and **access secret** in the data manager tool by setting this bash variables in a txt file : 
 
-Replace the placeholders with your scheme of interest (example : bordetella_1) your actual consumer token and secret :
+::
 
-"""
-coreprofiler db get_request_tokens --scheme <SCHEME_NAME> --consumer_key <YOUR_CONSUMER_TOKEN> --consumer_secret <YOUR_CONSUMER_SECRET>
-"""
+    export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>"
+    export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>"
+    export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>"
+    export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>"
 
-This command will provide you with a URL to visit in order to authorize client software to access your account. 
 
-After authorizing, it will give you a verification code that you need to enter in the command line prompt.
+6. Set the **path** to this txt file in your environment by making an environment variable 
+   * **pubMLST** example:
 
-It will then return your access token and secret.
+::
 
-5. Provide the consumer token, consumer secret, access token, and access secret in the data manager tool by setting this bash variables in a txt file : 
+    export PUBMLST_COREPROFILER_SECRETS_PATH="/path/to/your/secret_file_pubmlst.txt"
 
-"""
-export COREPROFILER_CONSUMER_TOKEN="<YOUR_CONSUMER_TOKEN>"
-export COREPROFILER_CONSUMER_SECRET="<YOUR_CONSUMER_SECRET>"
-export COREPROFILER_ACCESS_TOKEN="<YOUR_ACCESS_TOKEN>"
-export COREPROFILER_ACCESS_SECRET="<YOUR_ACCESS_SECRET>"
-"""
+   * **BIGSdb** example:
+
+::
 
-6. Set the path to this txt file in your environment by making an environment variable (example : export COREPROFILER_SECRETS_PATH="/path/to/your/secret_file.txt").
-    ]]></help>
+    export BIGSDB_COREPROFILER_SECRETS_PATH="/path/to/your/secret_file_bigsdb.txt"
+
+
+]]></help>
     <citations>
         <citation type="doi">10.3390/microorganisms10020292</citation>
     </citations>
--- a/test-data/coreprofiler_scheme.loc.test	Fri Nov 21 13:12:00 2025 +0000
+++ b/test-data/coreprofiler_scheme.loc.test	Mon Dec 08 11:36:13 2025 +0000
@@ -16,3 +16,10 @@
 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