# HG changeset patch
# User iuc
# Date 1681977103 0
# Node ID 97f310b8e308937250a43835911e86455a064175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
diff -r 000000000000 -r 97f310b8e308 data_manager/data_manager_fetch_pharokka_db.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_pharokka_db.py Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import subprocess
+import sys
+from datetime import datetime
+
+
+def main():
+ # Parse Command Line
+ parser = argparse.ArgumentParser(description="Create data manager JSON.")
+ parser.add_argument("--out", dest="output", action="store", help="JSON filename")
+ parser.add_argument("--version", dest="version", action="store", help="Version of the DB")
+ parser.add_argument(
+ "--test",
+ action="store_true",
+ help="option to test the script with an lighted database",
+ )
+
+ args = parser.parse_args()
+
+ # the output file of a DM is a json containing args that can be used by the DM
+ # most tools mainly use these args to find the extra_files_path for the DM, which can be used
+ # to store the DB data
+ with open(args.output) as fh:
+ params = json.load(fh)
+
+ workdir = params["output_data"][0]["extra_files_path"]
+ os.mkdir(workdir)
+
+ time = datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+ db_value = "db_from_{0}".format(time)
+ db_path = os.path.join(workdir, db_value)
+
+ # create DB
+ if args.test: # the test only checks that the pharokka download script is available and copies the test DB
+
+ # check if install_databases.py is there
+ command_args = ["install_databases.py", "-h"]
+ proc = subprocess.Popen(args=command_args, shell=False)
+ return_code = proc.wait()
+ if return_code:
+ print("Error downloading Pharokka database.", file=sys.stderr)
+ sys.exit(return_code)
+
+ # copy the test DB
+ test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "subset_pharokka_db")
+ command_args = ["cp", "-r", test_db_path, db_path]
+ else:
+ command_args = ["install_databases.py", "-o", db_path]
+
+ proc = subprocess.Popen(args=command_args, shell=False)
+ return_code = proc.wait()
+ if return_code:
+ print("Error downloading Pharokka database.", file=sys.stderr)
+ sys.exit(return_code)
+
+ # Update Data Manager JSON and write to file
+ data_manager_entry = {
+ "data_tables": {
+ "pharokka_db": {
+ "value": db_value,
+ "dbkey": db_value,
+ "version": args.version,
+ "name": f"Pharokka DB version {args.version} downloaded at {datetime.now()}",
+ "path": db_path,
+ }
+ }
+ }
+
+ with open(os.path.join(args.output), "w+") as fh:
+ json.dump(data_manager_entry, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 97f310b8e308 data_manager/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,35 @@
+
+
+ 1.3.0
+ 1
+ 22.05
+
+
+
+ pharokka
+
+
+
+
+
+ pharokka
+
+
+
+
+ pharokka.py --version
+
+
+
+
+
+ 10.1093/bioinformatics/btac776
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 97f310b8e308 data_manager/pharokka_db_fetcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/pharokka_db_fetcher.xml Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,41 @@
+
+
+
+ macros.xml
+
+
+
+
+ Fetches the DB required for phrokka
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/5Jan2023_data.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/5Jan2023_data.tsv Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,2 @@
+Accession Description Classification Genome Length (bp) Jumbophage molGC (%) Molecule Modification Date Number CDS Positive Strand (%) Negative Strand (%) Coding Capacity (%) Low Coding Capacity Warning tRNAs Host Lowest Taxa Genus Sub-family Family Order Class Phylum Kingdom Realm Baltimore Group Genbank Division Isolation Host (beware inconsistent and nonsense values)
+MF417929 Uncultured Caudovirales phage clone 2F_1 Uncultured Caudovirales phage clone 2F_1 Bracchivirus U2F1 Bracchivirus Peduoviridae Caudoviricetes Uroviricota Heunggongvirae Duplodnaviria Viruses 32618 FALSE 39.218 DNA 1-Nov-22 42 16.66666667 83.33333333 89.41688638 NA 0 Unspecified Bracchivirus Bracchivirus Unclassified Peduoviridae Caudovirales Caudoviricetes Uroviricota Heunggongvirae Duplodnaviria Group I ENV Unspecified
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/5Jan2023_genomes.fa.msh
Binary file data_manager/subset_pharokka_db/5Jan2023_genomes.fa.msh has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD
Binary file data_manager/subset_pharokka_db/CARD has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD.dbtype
Binary file data_manager/subset_pharokka_db/CARD.dbtype has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/CARD.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,2 @@
+0 0 298
+1 298 288
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD.lookup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/CARD.lookup Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,2 @@
+0 ACT97415.1 0
+1 AEJ08681.1 0
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD.source
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/CARD.source Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 protein_fasta_protein_homolog_model.fasta
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD_h
Binary file data_manager/subset_pharokka_db/CARD_h has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD_h.dbtype
Binary file data_manager/subset_pharokka_db/CARD_h.dbtype has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/CARD_h.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/CARD_h.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,2 @@
+0 0 75
+1 75 59
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/VFDB_setB_pro.fas
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/VFDB_setB_pro.fas Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,14 @@
+>VFG037170(gb|WP_001081754) (plc1) phospholipase C [Phospholipase C (VF0470) - Exotoxin (VFC0235)] [Acinetobacter baumannii 1656-2]
+MNRREFLLNSTKTMFGTAALASFPLSIQKALAIDAKVESGTIQDVKHIVILTQENRSFDN
+YFGTLKGVRGFGDRFTIPMTEGRKVWEQYDANKKKVLPYHLDSRLGNAQRVTGTNHSWSD
+GQGAWDNGRMSDWVAHKQPQSMGYYKKQEVEYQFALANAFTICDAYHCAMHAGTNPNRKF
+IWTGTNGPTGAGVASVVNEFDGIGPSTEGYEWTTYPERLQQAGVTWKVYQNMPDNFTDNP
+LAGFKQYRRANEQSGQPVSNDTLICLAYDEKIDATQPLYKGIANTMPDGGFLGAFKADIA
+QGKLPQVSWLVAPATYSEHPGPSSPVQGAWYIQEVLNALTENTQVWSQTVLLVNFDENDG
+FFDHVPSPSAPSKDINGVVYGKTTLTDQQVSYEYFNHPAVATSKSQPETDGRVYGPGVRV
+PMYVISPWSRGGWVNSQVFDHTSILQFLEKRFGVQEPNISPYRRAVCGDLTTAFNFKTPN
+LLPVAELDGKKTKAEADAIRVAQELLPQVSVPSQQQFPQQEIGIRPSRALPYILHTSAKV
+DVTQKTVKLMFSNTGKQAAVFHVYNRLDLTAIPRRYMVEAGKQLDDAWNTINGQYDLWVL
+GPNGFHRAFKGNLSQANQTQALPEIRVCVEECDANLYLKVRHDGNKSVKLNVKANAYLPN
+KTWMIETNSSEKELVWDMSEFGGWYDFTVTLADDATFSRRFAGRIETQEDSISDPYMGYL
+ES
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/aro_index.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/aro_index.tsv Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,3 @@
+ARO Accession CVTERM ID Model Sequence ID Model ID Model Name ARO Name Protein Accession DNA Accession AMR Gene Family Drug Class Resistance Mechanism CARD Short Name
+ARO:3001109 37489 1393 4 SHV-52 SHV-52 AEJ08681.1 HQ845196.1 SHV beta-lactamase carbapenem;cephalosporin;penam antibiotic inactivation SHV-52
+ARO:3002999 39433 1188 2 CblA-1 CblA-1 ACT97415.1 GQ343019.1 CblA beta-lactamase cephalosporin antibiotic inactivation CblA-1
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrog_annot_v4.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/phrog_annot_v4.tsv Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,2 @@
+phrog color annot category
+1 #fea328 integrase integration and excision
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrog_hhm_db
Binary file data_manager/subset_pharokka_db/phrog_hhm_db has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrog_hhm_db.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/phrog_hhm_db.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+phrog_1.hhm 0 95355
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_db
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_db.dbtype
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_db.index
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db
Binary file data_manager/subset_pharokka_db/phrogs_profile_db has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db.dbtype
Binary file data_manager/subset_pharokka_db/phrogs_profile_db.dbtype has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/phrogs_profile_db.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 0 15802
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_consensus
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_consensus.dbtype
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_consensus.index
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_h
Binary file data_manager/subset_pharokka_db/phrogs_profile_db_h has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_h.dbtype
Binary file data_manager/subset_pharokka_db/phrogs_profile_db_h.dbtype has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_h.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/phrogs_profile_db_h.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 0 18
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_seq
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_seq.dbtype
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_seq.index
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_seq_h
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/phrogs_profile_db_seq_h.index
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/protein_fasta_protein_homolog_model.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/protein_fasta_protein_homolog_model.fasta Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,4 @@
+>gb|ACT97415.1|ARO:3002999|CblA-1 [mixed culture bacterium AX_gF3SD01_15]
+MKAYFIAILTLFTCIATVVRAQQMSELENRIDSLLNGKKATVGIAVWTDKGDMLRYNDHVHFPLLSVFKFHVALAVLDKMDKQSISLDSIVSIKASQMPPNTYSPLRKKFPDQDFTITLRELMQYSISQSDNNACDILIEYAGGIKHINDYIHRLSIDSFNLSETEDGMHSSFEAVYRNWSTPSAMVRLLRTADEKELFSNKELKDFLWQTMIDTETGANKLKGMLPAKTVVGHKTGSSDRNADGMKTADNDAGLVILPDGRKYYIAAFVMDSYETDEDNANIIARISRMVYDAMR
+>gb|AEJ08681.1|ARO:3001109|SHV-52 [Klebsiella pneumoniae]
+MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb
Binary file data_manager/subset_pharokka_db/vfdb has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb.dbtype
Binary file data_manager/subset_pharokka_db/vfdb.dbtype has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/vfdb.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 0 724
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb.lookup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/vfdb.lookup Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 VFG037170(gb|WP_001081754) 0
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb.source
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/vfdb.source Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 VFDB_setB_pro.fas
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb_h
Binary file data_manager/subset_pharokka_db/vfdb_h has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb_h.dbtype
Binary file data_manager/subset_pharokka_db/vfdb_h.dbtype has changed
diff -r 000000000000 -r 97f310b8e308 data_manager/subset_pharokka_db/vfdb_h.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/subset_pharokka_db/vfdb_h.index Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,1 @@
+0 0 132
diff -r 000000000000 -r 97f310b8e308 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,23 @@
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 97f310b8e308 test-data/pharokka_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pharokka_db.loc Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,12 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a pharokka DB folder. The pharokka_db.loc
+#file needs this format (longer white space is the TAB character):
+
+#
+
+# for example:
+
+# pharokka_db pharokka_db v1.2.1 Pharokka Database v1.2.0 /data/pharokka_db
+
+# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or
+# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023)
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 tool-data/pharokka_db.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pharokka_db.loc Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,12 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a pharokka DB folder. The pharokka_db.loc
+#file needs this format (longer white space is the TAB character):
+
+#
+
+# for example:
+
+# pharokka_db pharokka_db v1.2.1 Pharokka Database v1.2.0 /data/pharokka_db
+
+# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or
+# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023)
\ No newline at end of file
diff -r 000000000000 -r 97f310b8e308 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, version, name, path
+
+
+
\ No newline at end of file