# 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 +]]> + +
+ + + + + + + + + + + + +
+
+ + + + + + + + + + + +
+
+ + +
+ +
+ + + not uncompressed + + + not uncompressed + + + uncompressed + + + + uncompressed + + + + uncompressed and file_choices['exclude_seq'] + + + + uncompressed and file_choices['exclude_genomic_cds'] + + + + uncompressed and file_choices['exclude_gff3'] + + + + uncompressed and file_choices['exclude_rna'] + + + + uncompressed and file_choices['exclude_protein'] + + + + uncompressed and file_choices['include_gbff'] + + + + uncompressed and file_choices['include_gtf'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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@" + + + + ncbi-datasets-cli + ca-certificates + p7zip + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $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}