# HG changeset patch
# User iuc
# Date 1643271647 0
# Node ID 1a7773882d2c430c33a2fe88d3bddd23f08a3a94
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
diff -r 000000000000 -r 1a7773882d2c datasets_genome.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datasets_genome.xml Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,215 @@
+
+ download genome sequence, annotation and metadata
+
+ macros.xml
+
+
+ ncbi_dataset.txt
+#end if
+]]>
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+ not uncompressed
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+ not uncompressed
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+ uncompressed
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+ uncompressed
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+ uncompressed and file_choices['exclude_seq']
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+ uncompressed and file_choices['exclude_genomic_cds']
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+ uncompressed and file_choices['exclude_gff3']
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+ uncompressed and file_choices['exclude_rna']
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+ uncompressed and file_choices['exclude_protein']
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+ uncompressed and file_choices['include_gbff']
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+ uncompressed and file_choices['include_gtf']
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diff -r 000000000000 -r 1a7773882d2c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,121 @@
+
+ 12.27.1
+ 20.01
+ MIT
+ profile="@PROFILE@" license="@LICENSE@"
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+
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+ ncbi-datasets-cli
+ ca-certificates
+ p7zip
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+ $file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq
+ $exclude_gene $exclude_protein $exclude_rna
+ $exclude_protein $exclude_pdb $exclude_gpff $exclude_cds
+ $exclude_seq @EXCLUDES_VIRUS_PROTEIN@
+
+
+
+ $file_choices.include_gbff $file_choices.include_gtf
+ $include_gbff
+
+
+
+ #if $filters.released_before:
+--released-before '$filters.released_before'
+#end if
+
+ #if $filters.released_since:
+--released-since '$filters.released_since'
+#end if
+
+
diff -r 000000000000 -r 1a7773882d2c test-data/GCF_000007445.1.genomic.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GCF_000007445.1.genomic.gtf Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+#gtf-version 2.2
+#!genome-build ASM744v1
+#!genome-build-accession NCBI_Assembly:GCF_000007445.1
+#!annotation-date 05/06/2021 17:43:00
+#!annotation-source NCBI RefSeq
+NC_004431.1 RefSeq gene 190 255 . + . gene_id "C_RS00005"; transcript_id ""; gbkey "Gene"; gene "thrL"; gene_biotype "protein_coding"; locus_tag "C_RS00005"; old_locus_tag "c5491";
+NC_004431.1 Protein Homology CDS 190 252 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "C_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11";
+NC_004431.1 Protein Homology start_codon 190 192 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "C_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11";
+NC_004431.1 Protein Homology stop_codon 253 255 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "C_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11";
+NC_004431.1 RefSeq gene 453 911 . + . gene_id "C_RS00010"; transcript_id ""; gbkey "Gene"; gene "tnpA"; gene_biotype "protein_coding"; locus_tag "C_RS00010"; old_locus_tag "c0002";
diff -r 000000000000 -r 1a7773882d2c test-data/accessions.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/accessions.txt Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,2 @@
+GCF_000013305.1
+GCF_000007445.1
diff -r 000000000000 -r 1a7773882d2c test-data/genome.2.GCF_000007445.1.genomic.cds
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.2.GCF_000007445.1.genomic.cds Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+>lcl|NC_004431.1_cds_WP_001386572.1_1 [gene=thrL] [locus_tag=C_RS00005] [protein=thr operon leader peptide] [protein_id=WP_001386572.1] [location=190..255] [gbkey=CDS]
+ATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGA
+>lcl|NC_004431.1_cds_WP_000526115.1_2 [gene=tnpA] [locus_tag=C_RS00010] [protein=IS200/IS605-like element IS200C family transposase] [protein_id=WP_000526115.1] [location=453..911] [gbkey=CDS]
+ATGGGGAACGAAAAGAGCTTAGCGCACACCCGATGGAACTGTAAATATCACATAGTATTTGCGCCAAAATACCGAAGACA
+GGTGTTCTACAGAGAGAAGCGTAGAGCAATAGGCTGTATTTTGAGAAAGCTGTGTGAGTGGAAAAGTGTACGGATTCTGG
+AAGCTGAATGCTGTGCAGATCATATCCATATGCTTGTGGAGATCCCGCCCAAAATGAGCGTATCAGGCTTTATGGGATAT
+CTGAAAGGGAAAAGCAGTCTGATGCCTTACGAGCAGTTTGGTGATTTGAAATTCAAATACAGGAACAGGGAGTTCTGGTG
+CAGAGGGTATTACGTCGATACGGTGGGTAAGAACACGGCGAAGATACAGGATTACATAAAGCACCAGCTTGAAGAGGATA
+AAATGGGAGAGCAGTTATCGATTCCCTATCCGGGCAGCCCGTTTACGGGCCGTAAGTAA
+>lcl|NC_004431.1_cds_WP_001264710.1_3 [gene=thrA] [locus_tag=C_RS00015] [protein=bifunctional aspartate kinase/homoserine dehydrogenase I] [protein_id=WP_001264710.1] [location=1048..3510] [gbkey=CDS]
diff -r 000000000000 -r 1a7773882d2c test-data/genome.2.GCF_000007445.1.seq.rpt.jsonl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.2.GCF_000007445.1.seq.rpt.jsonl Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,1 @@
+{"assemblyUnit":"GCF_000007455.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2640553","genbankAccession":"AE014075.1","length":5231428,"refseqAccession":"NC_004431.1","sortOrder":1}
diff -r 000000000000 -r 1a7773882d2c test-data/genome.2.GCF_000013305.1.genomic.cds
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.2.GCF_000013305.1.genomic.cds Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+>lcl|NC_008253.1_cds_WP_001386572.1_1 [gene=thrL] [locus_tag=ECP_RS00005] [protein=thr operon leader peptide] [protein_id=WP_001386572.1] [location=190..255] [gbkey=CDS]
+ATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGA
+>lcl|NC_008253.1_cds_WP_001264707.1_2 [gene=thrA] [locus_tag=ECP_RS00010] [protein=bifunctional aspartate kinase/homoserine dehydrogenase I] [protein_id=WP_001264707.1] [location=336..2798] [gbkey=CDS]
+ATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATATTCTGGAAAGCAA
+TGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCATCTGGTAGCGATGATTGAAAAAA
+CCATTAGCGGTCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGACGGGACTCGCCGCC
+GCCCAGCCGGGATTTCCGCTGGCACAATTGAAAACTTTCGTCGACCAGGAATTTGCCCAAATAAAACATGTCCTGCATGG
+CATCAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTA
+TGGCCGGCGTGTTAGAAGCGCGTGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGTCATTAC
+CTCGAATCTACCGTTGATATTGCTGAATCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGACCACATGGTGCTGAT
diff -r 000000000000 -r 1a7773882d2c test-data/genome.2.GCF_000013305.1.genomic.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.2.GCF_000013305.1.genomic.gtf Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+#gtf-version 2.2
+#!genome-build ASM1330v1
+#!genome-build-accession NCBI_Assembly:GCF_000013305.1
+#!annotation-date 05/06/2021 17:31:48
+#!annotation-source NCBI RefSeq
+NC_008253.1 RefSeq gene 190 255 . + . gene_id "ECP_RS00005"; transcript_id ""; gbkey "Gene"; gene "thrL"; gene_biotype "protein_coding"; locus_tag "ECP_RS00005"; old_locus_tag "ECP_0001";
+NC_008253.1 Protein Homology CDS 190 252 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "ECP_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11";
+NC_008253.1 Protein Homology start_codon 190 192 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "ECP_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11";
+NC_008253.1 Protein Homology stop_codon 253 255 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "ECP_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11";
+NC_008253.1 RefSeq gene 336 2798 . + . gene_id "ECP_RS00010"; transcript_id ""; gbkey "Gene"; gene "thrA"; gene_biotype "protein_coding"; locus_tag "ECP_RS00010"; old_locus_tag "ECP_0002";
diff -r 000000000000 -r 1a7773882d2c test-data/genome.2.GCF_000013305.1.seq.rpt.jsonl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.2.GCF_000013305.1.seq.rpt.jsonl Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,1 @@
+{"assemblyUnit":"GCF_000013315.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2495020","genbankAccession":"CP000247.1","length":4938920,"refseqAccession":"NC_008253.1","sortOrder":1}
diff -r 000000000000 -r 1a7773882d2c test-data/genome.3.GCF_000007445.1.genomic.gbff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.3.GCF_000007445.1.genomic.gbff Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+LOCUS NC_004431 5231428 bp DNA circular CON 13-MAY-2021
+DEFINITION Escherichia coli CFT073, complete sequence.
+ACCESSION NC_004431 NZ_AE016755 NZ_AE016756 NZ_AE016757 NZ_AE016758
+ NZ_AE016759 NZ_AE016760 NZ_AE016761 NZ_AE016762 NZ_AE016763
+ NZ_AE016764 NZ_AE016765 NZ_AE016766 NZ_AE016767 NZ_AE016768
+ NZ_AE016769 NZ_AE016770 NZ_AE016771 NZ_AE016772
+VERSION NC_004431.1
+DBLINK BioProject: PRJNA224116
+ BioSample: SAMN02604094
+ Assembly: GCF_000007445.1
diff -r 000000000000 -r 1a7773882d2c test-data/genome.3.GCF_000007445.1.genomic.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.3.GCF_000007445.1.genomic.gff Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM744v1
+#!genome-build-accession NCBI_Assembly:GCF_000007445.1
+#!annotation-date 05/06/2021 17:43:00
+#!annotation-source NCBI RefSeq
+##sequence-region NC_004431.1 1 5231428
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=199310
+NC_004431.1 RefSeq region 1 5231428 . + . ID=NC_004431.1:1..5231428;Dbxref=taxon:199310;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=CFT073
diff -r 000000000000 -r 1a7773882d2c test-data/genome.3.GCF_000007445.1.seq.rpt.jsonl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.3.GCF_000007445.1.seq.rpt.jsonl Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,1 @@
+{"assemblyUnit":"GCF_000007455.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2640553","genbankAccession":"AE014075.1","length":5231428,"refseqAccession":"NC_004431.1","sortOrder":1}
diff -r 000000000000 -r 1a7773882d2c test-data/genome.3.GCF_000013305.1.genomic.gbff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.3.GCF_000013305.1.genomic.gbff Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+LOCUS NC_008253 4938920 bp DNA circular CON 13-MAY-2021
+DEFINITION Escherichia coli 536, complete sequence.
+ACCESSION NC_008253
+VERSION NC_008253.1
+DBLINK BioProject: PRJNA224116
+ BioSample: SAMN02604181
+ Assembly: GCF_000013305.1
+KEYWORDS RefSeq.
+SOURCE Escherichia coli 536
+ ORGANISM Escherichia coli 536
diff -r 000000000000 -r 1a7773882d2c test-data/genome.3.GCF_000013305.1.genomic.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.3.GCF_000013305.1.genomic.gff Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM1330v1
+#!genome-build-accession NCBI_Assembly:GCF_000013305.1
+#!annotation-date 05/06/2021 17:31:48
+#!annotation-source NCBI RefSeq
+##sequence-region NC_008253.1 1 4938920
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=362663
+NC_008253.1 RefSeq region 1 4938920 . + . ID=NC_008253.1:1..4938920;Dbxref=taxon:362663;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;serogroup=O6:K15:H31;strain=536
diff -r 000000000000 -r 1a7773882d2c test-data/genome.3.GCF_000013305.1.seq.rpt.jsonl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.3.GCF_000013305.1.seq.rpt.jsonl Thu Jan 27 08:20:47 2022 +0000
@@ -0,0 +1,1 @@
+{"assemblyUnit":"GCF_000013315.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2495020","genbankAccession":"CP000247.1","length":4938920,"refseqAccession":"NC_008253.1","sortOrder":1}