# HG changeset patch
# User gga
# Date 1639129868 0
# Node ID c3251541cf2ba52429b852ebeee208fe5ea70282
# Parent b503fe85f261e14cb950bb1ffa262729ca60a68e
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"
diff -r b503fe85f261 -r c3251541cf2b export.py
--- a/export.py Tue Jun 08 09:16:01 2021 +0000
+++ b/export.py Fri Dec 10 09:51:08 2021 +0000
@@ -16,11 +16,13 @@
parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services')
CnOrGuess(parser)
parser.add_argument('--gff', type=argparse.FileType('w'))
+ parser.add_argument('--gff_with_fasta', action='store_true')
parser.add_argument('--fasta_pep', type=argparse.FileType('w'))
parser.add_argument('--fasta_cds', type=argparse.FileType('w'))
parser.add_argument('--fasta_cdna', type=argparse.FileType('w'))
parser.add_argument('--vcf', type=argparse.FileType('w'))
parser.add_argument('--json', type=argparse.FileType('w'))
+ parser.add_argument('--die', action='store_true')
parser.add_argument('email', help='User Email')
args = parser.parse_args()
@@ -39,6 +41,12 @@
all_orgs = []
all_orgs = [org['commonName'] for org in all_orgs]
+ def error(message):
+ if args.die:
+ raise Exception(message)
+ else:
+ print(message)
+
org_data = []
for org_cn in org_cns:
if org_cn not in all_orgs:
@@ -50,39 +58,58 @@
org = wa.organisms.show_organism(org_cn)
- uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs)
- if 'error' in uuid_gff or 'uuid' not in uuid_gff:
- raise Exception("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
- args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
+ # Fetch all the refseqs
+ realSeqs = wa.organisms.get_sequences(org['id'])
- time.sleep(1)
+ # We'll loop over them individually for decreased memory pressure
+ for sequence in realSeqs['sequences']:
+ print("Downloading", sequence)
- uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
- if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
- raise Exception("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
- args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
+ try:
+ uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=args.gff_with_fasta, sequences=[sequence['name']])
+ if 'error' in uuid_gff or 'uuid' not in uuid_gff:
+ error("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
+ args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
+ time.sleep(1)
+ except Exception as e:
+ error(e)
- time.sleep(1)
+ try:
+ uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=[sequence['name']])
+ if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
+ error("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
+ args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
+ time.sleep(1)
+ except Exception as e:
+ error(e)
- uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna')
- if 'error' in uuid_fa or 'uuid' not in uuid_fa:
- raise Exception("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
- args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
-
- time.sleep(1)
+ try:
+ uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='cdna')
+ if 'error' in uuid_fa or 'uuid' not in uuid_fa:
+ error("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
+ args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
+ time.sleep(1)
+ except Exception as e:
+ error(e)
- uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds')
- if 'error' in uuid_fa or 'uuid' not in uuid_fa:
- raise Exception("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
- args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
-
- time.sleep(1)
+ try:
+ uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='cds')
+ if 'error' in uuid_fa or 'uuid' not in uuid_fa:
+ error("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
+ args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
+ time.sleep(1)
+ except Exception as e:
+ error(e)
- uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide')
- if 'error' in uuid_fa or 'uuid' not in uuid_fa:
- raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
- args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
+ try:
+ uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=[sequence['name']], seq_type='peptide')
+ if 'error' in uuid_fa or 'uuid' not in uuid_fa:
+ error("Apollo failed to prepare the file for download: %s" % uuid_fa)
+ args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
+ time.sleep(1)
+ except Exception as e:
+ error(e)
- org_data.append(org)
+ org_data.append(org)
args.json.write(json.dumps(org_data, indent=2))
diff -r b503fe85f261 -r c3251541cf2b export.xml
--- a/export.xml Tue Jun 08 09:16:01 2021 +0000
+++ b/export.xml Fri Dec 10 09:51:08 2021 +0000
@@ -13,17 +13,21 @@
@ORG_CN_OR_GUESS@
--gff '$gff_out'
+$gff_with_fasta
--fasta_pep '$fasta_pep'
--fasta_cds '$fasta_cds'
--fasta_cdna '$fasta_cdna'
--vcf '$vcf_out'
--json '$json_out'
+$die
'$__user_email__'
]]>
+
+
diff -r b503fe85f261 -r c3251541cf2b macros.xml
--- a/macros.xml Tue Jun 08 09:16:01 2021 +0000
+++ b/macros.xml Fri Dec 10 09:51:08 2021 +0000
@@ -1,6 +1,6 @@
- 4.2.13
+ 4.2.13+galaxy0