Mercurial > repos > estrain > data_manager_fastani

changeset 25:4b7ed16c1095 draft

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Uploaded
author estrain
date Sat, 23 Jul 2022 01:22:42 +0000
parents 30c33c28b9fc
children b0c4144a9e5c
files data_manager_fastani/data_manager/data_manager_fastani.py data_manager_fastani/data_manager/data_manager_fastani.xml data_manager_fastani/tool-data/accessions.csv
diffstat 3 files changed, 118 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_fastani/data_manager/data_manager_fastani.py	Thu Jul 21 13:02:14 2022 +0000
+++ b/data_manager_fastani/data_manager/data_manager_fastani.py	Sat Jul 23 01:22:42 2022 +0000
@@ -89,7 +89,7 @@
     parser = argparse.ArgumentParser(description='Download FastANI Databases')
     parser.add_argument('--type', type=str, required=True, nargs=1, help='Database Type')
     parser.add_argument('--name', type=str, required=True, nargs=1, help='Unique Database Folder Name')
-    parser.add_argument('--acc', type=str, required=True, nargs=1, help='CSV Accession file with NCBI ftp folder IDs, see tool-data')
+    parser.add_argument('--acc', type=str, required=False, nargs=1, help='CSV Accession file with NCBI ftp folder IDs, see tool-data')
     parser.add_argument('--out', type=str, required=True, nargs=1, help='output file')
 
     args = parser.parse_args()
--- a/data_manager_fastani/data_manager/data_manager_fastani.xml	Thu Jul 21 13:02:14 2022 +0000
+++ b/data_manager_fastani/data_manager/data_manager_fastani.xml	Sat Jul 23 01:22:42 2022 +0000
@@ -1,15 +1,14 @@
-<tool id="data_manager_fastani" name="FastANI Data Manger" tool_type="manage_data" version="0.0.2" profile="20.01">
+<tool id="data_manager_fastani" name="FastANI Data Manger" tool_type="manage_data" version="0.0.1" profile="20.01">
     <requirements>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python $__tool_directory__/data_manager_fastani.py --type $input_source_selector --name $name --acc $accs --out ${output_file};
+        python $__tool_directory__/data_manager_fastani.py --type $input_source_selector --name $name --acc ../accessions.csv --out ${output_file};
     ]]></command>
     <inputs>
         <param name="input_source_selector" type="select" label="Database Selection">
           <option value="D1">FastANI D1</option>
           <option value="VL">FastANI D1 + VetLIRN Fish Pathogens</option>
         </param>
-	<param name="accs" type="data" format="csv" label="Accession CSV file"/>
         <param name="name" type="text" format="text" label="Database Name"/> 
     </inputs>
     <outputs>
--- a/data_manager_fastani/tool-data/accessions.csv	Thu Jul 21 13:02:14 2022 +0000
+++ b/data_manager_fastani/tool-data/accessions.csv	Sat Jul 23 01:22:42 2022 +0000
@@ -31,6 +31,121 @@
 Aeromonas_veronii,GCF_008693705.1_ASM869370v1
 Edwardsiella_piscicida,GCF_021733145.1_ASM2173314v1
 Staphylococcus_warneri,GCF_003571725.1_ASM357172v1
+Vibrio_aerogenes,GCF_900130105.1_Vibrio.aerogenes_CECT_7868_Velvet_Prokka
+Vibrio_aestuarianus,GCF_012395215.1_ASM1239521v1
+Vibrio_agarilyticus,GCF_012641465.1_ASM1264146v1
+Vibrio_albus,GCF_003144035.1_ASM314403v1
+Vibrio_alfacsensis,GCF_019670485.1_ASM1967048v1
+Vibrio_algicola,GCF_009601765.2_ASM960176v2
 Vibrio_alginolyticus,GCF_001471275.2_ASM147127v2
+Vibrio_algivorus,GCF_007623795.1_ASM762379v1
+Vibrio_antiquarius,GCF_000024825.1_ASM2482v1
+Vibrio_aphrogenes,GCF_002157735.2_ASM215773v2
+Vibrio_aquaticus,GCF_003970385.1_ASM397038v1
+Vibrio_aquimaris,GCF_009363415.1_ASM936341v1
+Vibrio_astriarenae,GCF_010587385.1_ASM1058738v1
+Vibrio_atlanticus,GCF_000091465.1_ASM9146v1
+Vibrio_atypicus,GCF_009811315.1_ASM981131v1
+Vibrio_azureus,GCF_002849855.1_ASM284985v1
+Vibrio_barjaei,GCF_001639065.2_ASM163906v2
+Vibrio_bathopelagicus,GCF_014879975.1_ASM1487997v1
+Vibrio_bivalvicida,GCF_001399455.2_ASM139945v2
+Vibrio_brasiliensis,GCF_000189255.1_ASM18925v1
+Vibrio_breoganii,GCF_002876585.1_ASM287658v1
+Vibrio_caribbeanicus,GCF_000165125.1_Vcar_1.0
+Vibrio_casei,GCF_003335255.1_ASM333525v1
+Vibrio_celticus,GCF_002156525.1_ASM215652v1
+Vibrio_chagasii,GCF_005281815.1_ASM528181v1
+Vibrio_chemaguriensis,GCF_012275705.1_ASM1227570v1
+Vibrio_cidicii,GCF_001597945.1_ASM159794v1
+Vibrio_cincinnatiensis,GCF_900460255.1_34500_B01
+Vibrio_comitans,GCF_006538565.1_ASM653856v1
+Vibrio_coralliilyticus,GCF_000967465.2_ASM96746v2
+Vibrio_coralliirubri,GCF_900379685.1_Vibrio_sp._strain_Evd3
+Vibrio_crassostreae,GCF_003751935.1_ASM375193v1
+Vibrio_cyclitrophicus,GCF_005144905.1_ASM514490v1
+Vibrio_diazotrophicus,GCF_002892925.1_ASM289292v1
+Vibrio_echinoideorum,GCF_004764665.1_ASM476466v1
+Vibrio_europaeus,GCF_001695575.1_ASM169557v1
+Vibrio_ezurae,GCF_003568985.1_Vezurae
+Vibrio_fluvialis,GCF_001558415.2_ASM155841v2
+Vibrio_fortis,GCF_000695685.1_Soap_denovo_2.01
+Vibrio_fujianensis,GCF_002749895.1_ASM274989v1
+Vibrio_galatheae,GCF_000967545.1_S2757
+Vibrio_gallaecicus,GCF_005281825.1_ASM528182v1
+Vibrio_gangliei,GCF_002934045.1_ASM293404v1
+Vibrio_gazogenes,GCF_002196515.1_ASM219651v1
+Vibrio_gigantis,GCF_022371215.1_ASM2237121v1
+Vibrio_halioticoli,GCF_003568965.1_Vhalioticoli
+Vibrio_hangzhouensis,GCF_900107935.1_IMG-taxon_2617270906_annotated_assembly
 Vibrio_harveyi,GCF_000770115.1_ASM77011v2
+Vibrio_hepatarius,GCF_001274785.1_ASM127478v1
+Vibrio_hibernica,GCF_015223435.1_ASM1522343v1
+Vibrio_hippocampi,GCF_921292975.1_V_hippocampi_CECT8226
+Vibrio_hyugaensis,GCF_002929865.1_ASM292986v1
+Vibrio_ichthyoenteri,GCF_000222605.1_ASM22260v1
+Vibrio_injensis,GCF_001895205.1_ASM189520v1
+Vibrio_inusitatus,GCF_006538525.1_ASM653852v1
+Vibrio_jasicida,GCF_002887615.1_ASM288761v1
+Vibrio_kanaloae,GCF_001995825.2_ASM199582v2
+Vibrio_lentus,GCF_002877605.2_ASM287760v2
+Vibrio_litoralis,GCF_000426765.1_ASM42676v1
+Vibrio_maerlii,GCF_003415655.1_ASM341565v1
+Vibrio_mangrovi,GCF_900184095.1_Vmangrovi_CECT7927_Spades_Prokka
+Vibrio_marinisediminis,GCF_014050145.1_ASM1405014v1
+Vibrio_marisflavi,GCF_921294215.1_V_marisflavi_CECT7928
+Vibrio_mediterranei,GCF_013364395.1_ASM1336439v1
+Vibrio_metoecus,GCF_001402675.1_ASM140267v1
+Vibrio_metschnikovii,GCF_009763765.1_ASM976376v1
+Vibrio_mexicanus,GCF_001012815.1_ASM101281v1
+Vibrio_mimicus,GCF_000176375.1_ASM17637v1
+Vibrio_mytili,GCF_000830505.1_ASM83050v1
+Vibrio_natriegens,GCF_001456255.1_ASM145625v1
+Vibrio_navarrensis,GCF_012275065.1_ASM1227506v1
+Vibrio_neptunius,GCF_000967495.1_S2394
+Vibrio_nereis,GCF_001591105.1_ASM159110v1
+Vibrio_nitrifigilis,GCF_015686695.1_ASM1568669v1
+Vibrio_orientalis,GCF_000176235.1_ASM17623v1
+Vibrio_ostreicida,GCF_001957165.1_ASM195716v1
+Vibrio_ouci,GCF_004551525.1_ASM455152v1
+Vibrio_owensii,GCF_002021755.1_ASM202175v1
+Vibrio_pacinii,GCF_000711795.1_ASM71179v1
+Vibrio_palustris,GCF_900162645.1_V_palustris_CECT9027T_Velvet_Prokka_EMBL
+Vibrio_panuliri,GCF_009938205.1_ASM993820v1
+Vibrio_paracholerae,GCF_003311965.1_ASM331196v1
+Vibrio_pectenicida,GCF_003937805.1_ASM393780v1
+Vibrio_penaeicida,GCF_019977755.1_ASM1997775v1
+Vibrio_plantisponsor,GCF_013041605.1_ASM1304160v1
+Vibrio_ponticus,GCF_009938225.1_ASM993822v1
+Vibrio_profundi,GCF_005281835.1_ASM528183v1
+Vibrio_proteolyticus,GCF_000467125.1_ASM46712v1
+Vibrio_qinghaiensis,GCF_002257545.1_ASM225754v1
+Vibrio_quintilis,GCF_900143745.1_V.quintilis_CECT7734T_Velvet_Prokka_EMBL
+Vibrio_renipiscarius,GCF_000827885.1_ASM82788v1
+Vibrio_rhizosphaerae,GCF_000711805.1_ASM71180v1
+Vibrio_rhodolitus,GCF_003350325.1_ASM335032v1
 Vibrio_rotiferianus,GCF_002214395.1_ASM221439v1
+Vibrio_ruber,GCF_900163965.1_V_ruber_CECT7878T_Velvet_Prokka_EMBL
+Vibrio_rumoiensis,GCF_002218045.2_ASM221804v2
+Vibrio_sagamiensis,GCF_007990935.1_ASM799093v1
+Vibrio_salilacus,GCF_002811245.1_ASM281124v1
+Vibrio_scophthalmi,GCF_001723385.1_ASM172338v1
+Vibrio_sinaloensis,GCF_023195835.1_ASM2319583v1
+Vibrio_sinensis,GCF_003605645.1_ASM360564v1
+Vibrio_sonorensis,GCF_001854765.1_ASM185476v1
+Vibrio_spartinae,GCF_014083925.1_ASM1408392v1
+Vibrio_splendidus,GCF_022812045.1_ASM2281204v1
+Vibrio_stylophorae,GCF_921293875.1_V_stylophorae_CECT7929
+Vibrio_superstes,GCF_003569005.1_Vsuperstes
+Vibrio_taketomensis,GCF_009938185.1_ASM993818v1
+Vibrio_tapetis,GCF_900233005.1_Vibrio_tapetis_CECT4600
+Vibrio_tetraodonis,GCF_003350295.1_ASM335029v1
+Vibrio_thalassae,GCF_900089835.1_VthalassaeCECT8203_Velvet_Prokka
+Vibrio_toranzoniae,GCF_900089765.1_VtoranzoniaeCECT7225_SPAdes_Prokka
+Vibrio_tritonius,GCF_001547935.1_ASM154793v1
+Vibrio_ulleungensis,GCF_016900875.1_ASM1690087v1
+Vibrio_variabilis,GCF_003263785.1_ASM326378v1
+Vibrio_viridaestus,GCF_003856525.1_ASM385652v1
+Vibrio_xiamenensis,GCF_900100015.1_IMG-taxon_2617270927_annotated_assembly
+Vibrio_zhugei,GCF_003716875.1_ASM371687v1
+Vibrio_ziniensis,GCF_011064285.1_ASM1106428v1