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Added a second test
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Harrison Deng 2025-02-21 22:14:07 +00:00
parent 7c0d209470
commit 52bd3ac07d
5 changed files with 182 additions and 17 deletions
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6
.vscode/tasks.json vendored
View File

@ -14,6 +14,12 @@
"type": "shell",
"command": "planemo serve",
"problemMatcher": []
},
{
"label": "run tests",
"type": "shell",
"command": "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html",
"problemMatcher": []
}
]
}

4
Jenkinsfile vendored
View File

@ -2,7 +2,7 @@ pipeline {
agent {
kubernetes {
cloud 'rsys-devel'
defaultContainer 'pip'
defaultContainer 'rootless-pip'
inheritFrom 'pip'
}
}
@ -11,6 +11,8 @@ pipeline {
stage ("install") {
steps {
sh 'pip install -r requirements.txt'
sh 'pip install standard-imghdr'
sh 'useradd galaxy -m'
}
}
stage ("lint") {

32
autobigs-cli.xml
View File

@ -1,4 +1,4 @@
<tool id="autobigs-cli" name="AutoBIGS.CLI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
<macros>
<token name="@TOOL_VERSION@">0.5.0</token>
@ -12,14 +12,14 @@
</requirements>
<command detect_errors="exit_code"><![CDATA[
#if $mode.operation == "info":
#if $select_info.retrieved == "schema":
#if $mode['operation'] == "info":
#if $select_info['retrieved'] == "schemas":
autoBIGS info $selected_schema --csv $info_out
#else if $select_info.retrieved == "databases":
#else if $select_info['retrieved'] == "databases":
autoBIGS info --retrieve-bigsdbs --csv $info_out
#end if
#else if $mode.operation == "st":
autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output"
#else if $mode['operation'] == "st":
autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
#end if
]]></command>
<inputs>
@ -30,13 +30,13 @@
</param>
<when value="info">
<conditional name="select_info">
<param name="retrieved" label="Schema or Database List" type="select">
<option value="schema">Available Schemas for Database</option>
<param name="retrieved" label="Schemas or Database List" type="select">
<option value="schemas">Available Schemas for Database</option>
<option value="databases">Available Databases</option>
</param>
<when value="schema">
<repeat name="schemas" title="Schemas" min="1">
<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="integer" min="0"/>
<when value="schemas">
<repeat name="schemas_list" title="Schemas" min="1">
<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="text"/>
</repeat>
</when>
<when value="databases">
@ -48,7 +48,7 @@
<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
<param name="stop_on_fail" argument="--sof" label="Stop on failure to match" value="false" type="boolean"/>
<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
</when>
</conditional>
</inputs>
@ -56,8 +56,8 @@
<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
<filter>mode['operation'] == "st"</filter>
</data>
<data name="info_out" label="${tool.name} supported databases/schemas" format="csv">
<filter>mode['operation'] == "info"</filter>
<data name="info_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter>
</data>
</outputs>
<tests>
@ -73,8 +73,8 @@
<param name="retrieved" value="databases" />
<output name="info_out">
<assert_contents>
<has_line line="BIGSdb Names,Source"/>
<has_line line="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
<has_text text="BIGSdb Names,Source"/>
<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
</assert_contents>
</output>
</test>

146
test-data/databases-2025-02-21.csv Normal file
View File

@ -0,0 +1,146 @@
BIGSdb Names,Source
pubmlst_aactinomycetemcomitans_seqdef,https://rest.pubmlst.org
pubmlst_abaumannii_seqdef,https://rest.pubmlst.org
pubmlst_achromobacter_seqdef,https://rest.pubmlst.org
pubmlst_aeromonas_seqdef,https://rest.pubmlst.org
pubmlst_afumigatus_seqdef,https://rest.pubmlst.org
pubmlst_aparagallinarum_seqdef,https://rest.pubmlst.org
pubmlst_aphagocytophilum_seqdef,https://rest.pubmlst.org
pubmlst_arcobacter_seqdef,https://rest.pubmlst.org
pubmlst_bbacilliformis_seqdef,https://rest.pubmlst.org
pubmlst_bcc_seqdef,https://rest.pubmlst.org
pubmlst_bcereus_seqdef,https://rest.pubmlst.org
pubmlst_bfragilis_seqdef,https://rest.pubmlst.org
pubmlst_bhenselae_seqdef,https://rest.pubmlst.org
pubmlst_blastocystis_seqdef,https://rest.pubmlst.org
pubmlst_blicheniformis_seqdef,https://rest.pubmlst.org
pubmlst_bmallei_seqdef,https://rest.pubmlst.org
pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api
pubmlst_borrelia_seqdef,https://rest.pubmlst.org
pubmlst_bpseudomallei_seqdef,https://rest.pubmlst.org
pubmlst_brachyspira_seqdef,https://rest.pubmlst.org
pubmlst_brucella_seqdef,https://rest.pubmlst.org
pubmlst_bsubtilis_seqdef,https://rest.pubmlst.org
pubmlst_bwashoensis_seqdef,https://rest.pubmlst.org
pubmlst_calbicans_seqdef,https://rest.pubmlst.org
pubmlst_campylobacter_nonjejuni_seqdef,https://rest.pubmlst.org
pubmlst_campylobacter_seqdef,https://rest.pubmlst.org
pubmlst_cbotulinum_seqdef,https://rest.pubmlst.org
pubmlst_cchauvoei_seqdef,https://rest.pubmlst.org
pubmlst_cdifficile_seqdef,https://rest.pubmlst.org
pubmlst_cfreundii_seqdef,https://rest.pubmlst.org
pubmlst_cglabrata_seqdef,https://rest.pubmlst.org
pubmlst_chlamydiales_seqdef,https://rest.pubmlst.org
pubmlst_ckrusei_seqdef,https://rest.pubmlst.org
pubmlst_cmaltaromaticum_seqdef,https://rest.pubmlst.org
pubmlst_cperfringens_seqdef,https://rest.pubmlst.org
pubmlst_cronobacter_seqdef,https://rest.pubmlst.org
pubmlst_csepticum_seqdef,https://rest.pubmlst.org
pubmlst_csinensis_seqdef,https://rest.pubmlst.org
pubmlst_ctropicalis_seqdef,https://rest.pubmlst.org
pubmlst_diphtheria_seqdef,https://bigsdb.pasteur.fr/api
pubmlst_dnodosus_seqdef,https://rest.pubmlst.org
pubmlst_ecloacae_seqdef,https://rest.pubmlst.org
pubmlst_edwardsiella_seqdef,https://rest.pubmlst.org
pubmlst_efaecalis_seqdef,https://rest.pubmlst.org
pubmlst_efaecium_seqdef,https://rest.pubmlst.org
pubmlst_escherichia_seqdef,https://rest.pubmlst.org
pubmlst_fpsychrophilum_seqdef,https://rest.pubmlst.org
pubmlst_gallibacterium_seqdef,https://rest.pubmlst.org
pubmlst_geotrichum_seqdef,https://rest.pubmlst.org
pubmlst_hcinaedi_seqdef,https://rest.pubmlst.org
pubmlst_helicobacter_seqdef,https://rest.pubmlst.org
pubmlst_hinfluenzae_seqdef,https://rest.pubmlst.org
pubmlst_hparasuis_seqdef,https://rest.pubmlst.org
pubmlst_hsuis_seqdef,https://rest.pubmlst.org
pubmlst_kaerogenes_seqdef,https://rest.pubmlst.org
pubmlst_klebsiella_seqdef,https://bigsdb.pasteur.fr/api
pubmlst_koxytoca_seqdef,https://rest.pubmlst.org
pubmlst_kseptempunctata_seqdef,https://rest.pubmlst.org
pubmlst_leptospira_seqdef,https://rest.pubmlst.org
pubmlst_lgarvieae_seqdef,https://rest.pubmlst.org
pubmlst_liberibacter_seqdef,https://rest.pubmlst.org
pubmlst_listeria_seqdef,https://bigsdb.pasteur.fr/api
pubmlst_llactis_phage_seqdef,https://rest.pubmlst.org
pubmlst_lsalivarius_seqdef,https://rest.pubmlst.org
pubmlst_mabscessus_seqdef,https://rest.pubmlst.org
pubmlst_magalactiae_seqdef,https://rest.pubmlst.org
pubmlst_manserisalpingitidis_seqdef,https://rest.pubmlst.org
pubmlst_mbovis_seqdef,https://rest.pubmlst.org
pubmlst_mcanis_seqdef,https://rest.pubmlst.org
pubmlst_mcaseolyticus_seqdef,https://rest.pubmlst.org
pubmlst_mflocculare_seqdef,https://rest.pubmlst.org
pubmlst_mgallisepticum_seqdef,https://rest.pubmlst.org
pubmlst_mgenitalium_seqdef,https://rest.pubmlst.org
pubmlst_mhaemolytica_seqdef,https://rest.pubmlst.org
pubmlst_mhominis_seqdef,https://rest.pubmlst.org
pubmlst_mhyopneumoniae_seqdef,https://rest.pubmlst.org
pubmlst_mhyorhinis_seqdef,https://rest.pubmlst.org
pubmlst_mhyosynoviae_seqdef,https://rest.pubmlst.org
pubmlst_miowae_seqdef,https://rest.pubmlst.org
pubmlst_mplutonius_seqdef,https://rest.pubmlst.org
pubmlst_mpneumoniae_seqdef,https://rest.pubmlst.org
pubmlst_msciuri_seqdef,https://rest.pubmlst.org
pubmlst_msynoviae_seqdef,https://rest.pubmlst.org
pubmlst_mycobacteria_seqdef,https://rest.pubmlst.org
pubmlst_neisseria_seqdef,https://rest.pubmlst.org
pubmlst_oralstrep_seqdef,https://rest.pubmlst.org
pubmlst_orhinotracheale_seqdef,https://rest.pubmlst.org
pubmlst_otsutsugamushi_seqdef,https://rest.pubmlst.org
pubmlst_pacnes_seqdef,https://rest.pubmlst.org
pubmlst_paeruginosa_seqdef,https://rest.pubmlst.org
pubmlst_pdamselae_seqdef,https://rest.pubmlst.org
pubmlst_pfluorescens_seqdef,https://rest.pubmlst.org
pubmlst_pgingivalis_seqdef,https://rest.pubmlst.org
pubmlst_plarvae_seqdef,https://rest.pubmlst.org
pubmlst_plasmid_seqdef,https://rest.pubmlst.org
pubmlst_pmultocida_seqdef,https://rest.pubmlst.org
pubmlst_ppentosaceus_seqdef,https://rest.pubmlst.org
pubmlst_pputida_seqdef,https://rest.pubmlst.org
pubmlst_proteus_seqdef,https://rest.pubmlst.org
pubmlst_psalmonis_seqdef,https://rest.pubmlst.org
pubmlst_ranatipestifer_seqdef,https://rest.pubmlst.org
pubmlst_rhodococcus_seqdef,https://rest.pubmlst.org
pubmlst_rmlst_seqdef,https://rest.pubmlst.org
pubmlst_sagalactiae_seqdef,https://rest.pubmlst.org
pubmlst_salmonella_seqdef,https://rest.pubmlst.org
pubmlst_saureus_seqdef,https://rest.pubmlst.org
pubmlst_sbsec_seqdef,https://rest.pubmlst.org
pubmlst_scanis_seqdef,https://rest.pubmlst.org
pubmlst_schromogenes_seqdef,https://rest.pubmlst.org
pubmlst_sdysgalactiae_seqdef,https://rest.pubmlst.org
pubmlst_sepidermidis_seqdef,https://rest.pubmlst.org
pubmlst_serratia_seqdef,https://rest.pubmlst.org
pubmlst_sgallolyticus_seqdef,https://rest.pubmlst.org
pubmlst_shaemolyticus_seqdef,https://rest.pubmlst.org
pubmlst_shewanella_seqdef,https://rest.pubmlst.org
pubmlst_shominis_seqdef,https://rest.pubmlst.org
pubmlst_siniae_seqdef,https://rest.pubmlst.org
pubmlst_sinorhizobium_seqdef,https://rest.pubmlst.org
pubmlst_smaltophilia_seqdef,https://rest.pubmlst.org
pubmlst_smitis_seqdef,https://rest.pubmlst.org
pubmlst_sparasitica_seqdef,https://rest.pubmlst.org
pubmlst_spneumoniae_seqdef,https://rest.pubmlst.org
pubmlst_spseudintermedius_seqdef,https://rest.pubmlst.org
pubmlst_spyogenes_seqdef,https://rest.pubmlst.org
pubmlst_ssuis_seqdef,https://rest.pubmlst.org
pubmlst_sthermophilus_seqdef,https://rest.pubmlst.org
pubmlst_streptomyces_seqdef,https://rest.pubmlst.org
pubmlst_suberis_seqdef,https://rest.pubmlst.org
pubmlst_szooepidemicus_seqdef,https://rest.pubmlst.org
pubmlst_taylorella_seqdef,https://rest.pubmlst.org
pubmlst_tenacibaculum_seqdef,https://rest.pubmlst.org
pubmlst_test_seqdef,https://rest.pubmlst.org
pubmlst_tpallidum_seqdef,https://rest.pubmlst.org
pubmlst_tvaginalis_seqdef,https://rest.pubmlst.org
pubmlst_ureaplasma_seqdef,https://rest.pubmlst.org
pubmlst_vcholerae_seqdef,https://rest.pubmlst.org
pubmlst_vibrio_seqdef,https://rest.pubmlst.org
pubmlst_vparahaemolyticus_seqdef,https://rest.pubmlst.org
pubmlst_vtapetis_seqdef,https://rest.pubmlst.org
pubmlst_vvulnificus_seqdef,https://rest.pubmlst.org
pubmlst_wolbachia_seqdef,https://rest.pubmlst.org
pubmlst_xcitri_seqdef,https://rest.pubmlst.org
pubmlst_xfastidiosa_seqdef,https://rest.pubmlst.org
pubmlst_yersinia_seqdef,https://bigsdb.pasteur.fr/api
pubmlst_yruckeri_seqdef,https://rest.pubmlst.org
1 BIGSdb Names Source
2 pubmlst_aactinomycetemcomitans_seqdef https://rest.pubmlst.org
3 pubmlst_abaumannii_seqdef https://rest.pubmlst.org
4 pubmlst_achromobacter_seqdef https://rest.pubmlst.org
5 pubmlst_aeromonas_seqdef https://rest.pubmlst.org
6 pubmlst_afumigatus_seqdef https://rest.pubmlst.org
7 pubmlst_aparagallinarum_seqdef https://rest.pubmlst.org
8 pubmlst_aphagocytophilum_seqdef https://rest.pubmlst.org
9 pubmlst_arcobacter_seqdef https://rest.pubmlst.org
10 pubmlst_bbacilliformis_seqdef https://rest.pubmlst.org
11 pubmlst_bcc_seqdef https://rest.pubmlst.org
12 pubmlst_bcereus_seqdef https://rest.pubmlst.org
13 pubmlst_bfragilis_seqdef https://rest.pubmlst.org
14 pubmlst_bhenselae_seqdef https://rest.pubmlst.org
15 pubmlst_blastocystis_seqdef https://rest.pubmlst.org
16 pubmlst_blicheniformis_seqdef https://rest.pubmlst.org
17 pubmlst_bmallei_seqdef https://rest.pubmlst.org
18 pubmlst_bordetella_seqdef https://bigsdb.pasteur.fr/api
19 pubmlst_borrelia_seqdef https://rest.pubmlst.org
20 pubmlst_bpseudomallei_seqdef https://rest.pubmlst.org
21 pubmlst_brachyspira_seqdef https://rest.pubmlst.org
22 pubmlst_brucella_seqdef https://rest.pubmlst.org
23 pubmlst_bsubtilis_seqdef https://rest.pubmlst.org
24 pubmlst_bwashoensis_seqdef https://rest.pubmlst.org
25 pubmlst_calbicans_seqdef https://rest.pubmlst.org
26 pubmlst_campylobacter_nonjejuni_seqdef https://rest.pubmlst.org
27 pubmlst_campylobacter_seqdef https://rest.pubmlst.org
28 pubmlst_cbotulinum_seqdef https://rest.pubmlst.org
29 pubmlst_cchauvoei_seqdef https://rest.pubmlst.org
30 pubmlst_cdifficile_seqdef https://rest.pubmlst.org
31 pubmlst_cfreundii_seqdef https://rest.pubmlst.org
32 pubmlst_cglabrata_seqdef https://rest.pubmlst.org
33 pubmlst_chlamydiales_seqdef https://rest.pubmlst.org
34 pubmlst_ckrusei_seqdef https://rest.pubmlst.org
35 pubmlst_cmaltaromaticum_seqdef https://rest.pubmlst.org
36 pubmlst_cperfringens_seqdef https://rest.pubmlst.org
37 pubmlst_cronobacter_seqdef https://rest.pubmlst.org
38 pubmlst_csepticum_seqdef https://rest.pubmlst.org
39 pubmlst_csinensis_seqdef https://rest.pubmlst.org
40 pubmlst_ctropicalis_seqdef https://rest.pubmlst.org
41 pubmlst_diphtheria_seqdef https://bigsdb.pasteur.fr/api
42 pubmlst_dnodosus_seqdef https://rest.pubmlst.org
43 pubmlst_ecloacae_seqdef https://rest.pubmlst.org
44 pubmlst_edwardsiella_seqdef https://rest.pubmlst.org
45 pubmlst_efaecalis_seqdef https://rest.pubmlst.org
46 pubmlst_efaecium_seqdef https://rest.pubmlst.org
47 pubmlst_escherichia_seqdef https://rest.pubmlst.org
48 pubmlst_fpsychrophilum_seqdef https://rest.pubmlst.org
49 pubmlst_gallibacterium_seqdef https://rest.pubmlst.org
50 pubmlst_geotrichum_seqdef https://rest.pubmlst.org
51 pubmlst_hcinaedi_seqdef https://rest.pubmlst.org
52 pubmlst_helicobacter_seqdef https://rest.pubmlst.org
53 pubmlst_hinfluenzae_seqdef https://rest.pubmlst.org
54 pubmlst_hparasuis_seqdef https://rest.pubmlst.org
55 pubmlst_hsuis_seqdef https://rest.pubmlst.org
56 pubmlst_kaerogenes_seqdef https://rest.pubmlst.org
57 pubmlst_klebsiella_seqdef https://bigsdb.pasteur.fr/api
58 pubmlst_koxytoca_seqdef https://rest.pubmlst.org
59 pubmlst_kseptempunctata_seqdef https://rest.pubmlst.org
60 pubmlst_leptospira_seqdef https://rest.pubmlst.org
61 pubmlst_lgarvieae_seqdef https://rest.pubmlst.org
62 pubmlst_liberibacter_seqdef https://rest.pubmlst.org
63 pubmlst_listeria_seqdef https://bigsdb.pasteur.fr/api
64 pubmlst_llactis_phage_seqdef https://rest.pubmlst.org
65 pubmlst_lsalivarius_seqdef https://rest.pubmlst.org
66 pubmlst_mabscessus_seqdef https://rest.pubmlst.org
67 pubmlst_magalactiae_seqdef https://rest.pubmlst.org
68 pubmlst_manserisalpingitidis_seqdef https://rest.pubmlst.org
69 pubmlst_mbovis_seqdef https://rest.pubmlst.org
70 pubmlst_mcanis_seqdef https://rest.pubmlst.org
71 pubmlst_mcaseolyticus_seqdef https://rest.pubmlst.org
72 pubmlst_mflocculare_seqdef https://rest.pubmlst.org
73 pubmlst_mgallisepticum_seqdef https://rest.pubmlst.org
74 pubmlst_mgenitalium_seqdef https://rest.pubmlst.org
75 pubmlst_mhaemolytica_seqdef https://rest.pubmlst.org
76 pubmlst_mhominis_seqdef https://rest.pubmlst.org
77 pubmlst_mhyopneumoniae_seqdef https://rest.pubmlst.org
78 pubmlst_mhyorhinis_seqdef https://rest.pubmlst.org
79 pubmlst_mhyosynoviae_seqdef https://rest.pubmlst.org
80 pubmlst_miowae_seqdef https://rest.pubmlst.org
81 pubmlst_mplutonius_seqdef https://rest.pubmlst.org
82 pubmlst_mpneumoniae_seqdef https://rest.pubmlst.org
83 pubmlst_msciuri_seqdef https://rest.pubmlst.org
84 pubmlst_msynoviae_seqdef https://rest.pubmlst.org
85 pubmlst_mycobacteria_seqdef https://rest.pubmlst.org
86 pubmlst_neisseria_seqdef https://rest.pubmlst.org
87 pubmlst_oralstrep_seqdef https://rest.pubmlst.org
88 pubmlst_orhinotracheale_seqdef https://rest.pubmlst.org
89 pubmlst_otsutsugamushi_seqdef https://rest.pubmlst.org
90 pubmlst_pacnes_seqdef https://rest.pubmlst.org
91 pubmlst_paeruginosa_seqdef https://rest.pubmlst.org
92 pubmlst_pdamselae_seqdef https://rest.pubmlst.org
93 pubmlst_pfluorescens_seqdef https://rest.pubmlst.org
94 pubmlst_pgingivalis_seqdef https://rest.pubmlst.org
95 pubmlst_plarvae_seqdef https://rest.pubmlst.org
96 pubmlst_plasmid_seqdef https://rest.pubmlst.org
97 pubmlst_pmultocida_seqdef https://rest.pubmlst.org
98 pubmlst_ppentosaceus_seqdef https://rest.pubmlst.org
99 pubmlst_pputida_seqdef https://rest.pubmlst.org
100 pubmlst_proteus_seqdef https://rest.pubmlst.org
101 pubmlst_psalmonis_seqdef https://rest.pubmlst.org
102 pubmlst_ranatipestifer_seqdef https://rest.pubmlst.org
103 pubmlst_rhodococcus_seqdef https://rest.pubmlst.org
104 pubmlst_rmlst_seqdef https://rest.pubmlst.org
105 pubmlst_sagalactiae_seqdef https://rest.pubmlst.org
106 pubmlst_salmonella_seqdef https://rest.pubmlst.org
107 pubmlst_saureus_seqdef https://rest.pubmlst.org
108 pubmlst_sbsec_seqdef https://rest.pubmlst.org
109 pubmlst_scanis_seqdef https://rest.pubmlst.org
110 pubmlst_schromogenes_seqdef https://rest.pubmlst.org
111 pubmlst_sdysgalactiae_seqdef https://rest.pubmlst.org
112 pubmlst_sepidermidis_seqdef https://rest.pubmlst.org
113 pubmlst_serratia_seqdef https://rest.pubmlst.org
114 pubmlst_sgallolyticus_seqdef https://rest.pubmlst.org
115 pubmlst_shaemolyticus_seqdef https://rest.pubmlst.org
116 pubmlst_shewanella_seqdef https://rest.pubmlst.org
117 pubmlst_shominis_seqdef https://rest.pubmlst.org
118 pubmlst_siniae_seqdef https://rest.pubmlst.org
119 pubmlst_sinorhizobium_seqdef https://rest.pubmlst.org
120 pubmlst_smaltophilia_seqdef https://rest.pubmlst.org
121 pubmlst_smitis_seqdef https://rest.pubmlst.org
122 pubmlst_sparasitica_seqdef https://rest.pubmlst.org
123 pubmlst_spneumoniae_seqdef https://rest.pubmlst.org
124 pubmlst_spseudintermedius_seqdef https://rest.pubmlst.org
125 pubmlst_spyogenes_seqdef https://rest.pubmlst.org
126 pubmlst_ssuis_seqdef https://rest.pubmlst.org
127 pubmlst_sthermophilus_seqdef https://rest.pubmlst.org
128 pubmlst_streptomyces_seqdef https://rest.pubmlst.org
129 pubmlst_suberis_seqdef https://rest.pubmlst.org
130 pubmlst_szooepidemicus_seqdef https://rest.pubmlst.org
131 pubmlst_taylorella_seqdef https://rest.pubmlst.org
132 pubmlst_tenacibaculum_seqdef https://rest.pubmlst.org
133 pubmlst_test_seqdef https://rest.pubmlst.org
134 pubmlst_tpallidum_seqdef https://rest.pubmlst.org
135 pubmlst_tvaginalis_seqdef https://rest.pubmlst.org
136 pubmlst_ureaplasma_seqdef https://rest.pubmlst.org
137 pubmlst_vcholerae_seqdef https://rest.pubmlst.org
138 pubmlst_vibrio_seqdef https://rest.pubmlst.org
139 pubmlst_vparahaemolyticus_seqdef https://rest.pubmlst.org
140 pubmlst_vtapetis_seqdef https://rest.pubmlst.org
141 pubmlst_vvulnificus_seqdef https://rest.pubmlst.org
142 pubmlst_wolbachia_seqdef https://rest.pubmlst.org
143 pubmlst_xcitri_seqdef https://rest.pubmlst.org
144 pubmlst_xfastidiosa_seqdef https://rest.pubmlst.org
145 pubmlst_yersinia_seqdef https://bigsdb.pasteur.fr/api
146 pubmlst_yruckeri_seqdef https://rest.pubmlst.org

11
test-data/schemas-2025-02-21.csv Normal file
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@ -0,0 +1,11 @@
Name,ID
Autotransporters,11
Bp_vaccine antigens,7
MLST,3
Other toxins,9
PRN-test-Bp,5
Phase,8
T3SS,10
cgMLST_genus,1
cgMLST_pertussis,4
macrolide resistance,6
1 Name ID
2 Autotransporters 11
3 Bp_vaccine antigens 7
4 MLST 3
5 Other toxins 9
6 PRN-test-Bp 5
7 Phase 8
8 T3SS 10
9 cgMLST_genus 1
10 cgMLST_pertussis 4
11 macrolide resistance 6