Mercurial > repos > iuc > data_manager_build_coreprofiler
changeset 3:9e6d0309ec06 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit 31b55c90f2a622c8dceb93bb1142c46c43989d59
| author | iuc |
|---|---|
| date | Fri, 12 Dec 2025 21:37:42 +0000 |
| parents | c80b2251cb78 |
| children | 45c8bfaab608 |
| files | data_manager/data_manager_build_coreprofiler_download.xml test-data/coreprofiler_scheme.loc.test |
| diffstat | 2 files changed, 143 insertions(+), 68 deletions(-) [+] |
line wrap: on
line diff
--- 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
--- 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