# HG changeset patch # User iuc # Date 1651670143 0 # Node ID 6c829a430475a5dd8a3e011a3b1774873f5eb8f1 # Parent c47a0a93ffd2fe1c34e93428aba0ed76d58e8b4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6" diff -r c47a0a93ffd2 -r 6c829a430475 datasets_genome.xml --- a/datasets_genome.xml Mon Mar 07 12:05:56 2022 +0000 +++ b/datasets_genome.xml Wed May 04 13:15:43 2022 +0000 @@ -19,10 +19,10 @@ $filters.reference $filters.annotated #if $filters.assembly_level: ---assembly_level $filters.assembly_level +--assembly-level $filters.assembly_level #end if #if $filters.assembly_source: ---assembly_source $filters.assembly_source +--assembly-source $filters.assembly_source #end if #if $filters.chromosomes: --chromosomes '$filters.chromosomes' @@ -68,7 +68,7 @@ -
+
@@ -90,23 +90,23 @@ - uncompressed and file_choices['exclude_seq'] + uncompressed and not file_choices['exclude_seq'] - uncompressed and file_choices['exclude_genomic_cds'] + uncompressed and not file_choices['exclude_genomic_cds'] - uncompressed and file_choices['exclude_gff3'] + uncompressed and not file_choices['exclude_gff3'] - uncompressed and file_choices['exclude_rna'] + uncompressed and not file_choices['exclude_rna'] - uncompressed and file_choices['exclude_protein'] + uncompressed and not file_choices['exclude_protein'] @@ -125,6 +125,11 @@ + + + + + @@ -133,7 +138,28 @@ - + + + + + + + + + + + + + + + + + + + + + + @@ -143,17 +169,16 @@ - + + + + - - - - @@ -172,8 +197,10 @@ - - + + + + @@ -181,10 +208,6 @@ - - - - @@ -194,6 +217,25 @@ + + + + + + + + + + + + + + + + + + + diff -r c47a0a93ffd2 -r 6c829a430475 macros.xml --- a/macros.xml Mon Mar 07 12:05:56 2022 +0000 +++ b/macros.xml Wed May 04 13:15:43 2022 +0000 @@ -1,5 +1,5 @@ - 13.4.0 + 13.14.0 20.01 MIT profile="@PROFILE@" license="@LICENSE@" @@ -68,18 +68,15 @@ - - - - - + + - - - - - + + + + + diff -r c47a0a93ffd2 -r 6c829a430475 test-data/GCF_000001405.40.seq.rpt.jsonl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GCF_000001405.40.seq.rpt.jsonl Wed May 04 13:15:43 2022 +0000 @@ -0,0 +1,191 @@ +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","gcCount":"103674491","genbankAccession":"CM000663.2","length":248956422,"refseqAccession":"NC_000001.11","role":"assembled-molecule","sortOrder":1,"ucscStyleName":"chr1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270706.1","length":175055,"refseqAccession":"NT_187361.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270706v1_random"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270707.1","length":32032,"refseqAccession":"NT_187362.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270707v1_random"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270708.1","length":127682,"refseqAccession":"NT_187363.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270708v1_random"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270709.1","length":66860,"refseqAccession":"NT_187364.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270709v1_random"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270710.1","length":40176,"refseqAccession":"NT_187365.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270710v1_random"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270711.1","length":42210,"refseqAccession":"NT_187366.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270711v1_random"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270712.1","length":176043,"refseqAccession":"NT_187367.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270712v1_random"} 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+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270589.1","length":44474,"refseqAccession":"NT_187451.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270589v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270590.1","length":4685,"refseqAccession":"NT_187452.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270590v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270591.1","length":5796,"refseqAccession":"NT_187457.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270591v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270593.1","length":3041,"refseqAccession":"NT_187456.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270593v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270741.1","length":157432,"refseqAccession":"NT_187497.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270741v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270742.1","length":186739,"refseqAccession":"NT_187513.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270742v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270743.1","length":210658,"refseqAccession":"NT_187498.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270743v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270744.1","length":168472,"refseqAccession":"NT_187499.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270744v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270745.1","length":41891,"refseqAccession":"NT_187500.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270745v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270746.1","length":66486,"refseqAccession":"NT_187501.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270746v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270747.1","length":198735,"refseqAccession":"NT_187502.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270747v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270748.1","length":93321,"refseqAccession":"NT_187503.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270748v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270749.1","length":158759,"refseqAccession":"NT_187504.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270749v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270750.1","length":148850,"refseqAccession":"NT_187505.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270750v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270751.1","length":150742,"refseqAccession":"NT_187506.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270751v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270753.1","length":62944,"refseqAccession":"NT_187508.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270753v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270754.1","length":40191,"refseqAccession":"NT_187509.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270754v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270755.1","length":36723,"refseqAccession":"NT_187510.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270755v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270756.1","length":79590,"refseqAccession":"NT_187511.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270756v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270757.1","length":71251,"refseqAccession":"NT_187512.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270757v1"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"X","gcCount":"67807309","genbankAccession":"CM000685.2","length":156040895,"refseqAccession":"NC_000023.11","role":"assembled-molecule","sortOrder":23,"ucscStyleName":"chrX"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Y","gcCount":"10963787","genbankAccession":"CM000686.2","length":57227415,"refseqAccession":"NC_000024.10","role":"assembled-molecule","sortOrder":24,"ucscStyleName":"chrY"} +{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Y","genbankAccession":"KI270740.1","length":37240,"refseqAccession":"NT_187395.1","role":"unlocalized-scaffold","sortOrder":24,"ucscStyleName":"chrY_KI270740v1_random"} +{"assemblyUnit":"GCF_000006015.1","assignedMoleculeLocationType":"Mitochondrion","chrName":"MT","gcCount":"7350","genbankAccession":"J01415.2","length":16569,"refseqAccession":"NC_012920.1","role":"assembled-molecule","sortOrder":1,"ucscStyleName":"chrM"} diff -r c47a0a93ffd2 -r 6c829a430475 test-data/GCF_000007445.1.genomic.gtf --- a/test-data/GCF_000007445.1.genomic.gtf Mon Mar 07 12:05:56 2022 +0000 +++ b/test-data/GCF_000007445.1.genomic.gtf Wed May 04 13:15:43 2022 +0000 @@ -1,7 +1,3 @@ -#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"; diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.2.GCF_000007445.1.seq.rpt.jsonl --- a/test-data/genome.2.GCF_000007445.1.seq.rpt.jsonl Mon Mar 07 12:05:56 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"assemblyUnit":"GCF_000007455.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2640553","genbankAccession":"AE014075.1","length":5231428,"refseqAccession":"NC_004431.1","sortOrder":1} diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.2.GCF_000013305.1.genomic.gtf --- a/test-data/genome.2.GCF_000013305.1.genomic.gtf Mon Mar 07 12:05:56 2022 +0000 +++ b/test-data/genome.2.GCF_000013305.1.genomic.gtf Wed May 04 13:15:43 2022 +0000 @@ -1,7 +1,3 @@ -#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"; diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.2.GCF_000013305.1.seq.rpt.jsonl --- a/test-data/genome.2.GCF_000013305.1.seq.rpt.jsonl Mon Mar 07 12:05:56 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"assemblyUnit":"GCF_000013315.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2495020","genbankAccession":"CP000247.1","length":4938920,"refseqAccession":"NC_008253.1","sortOrder":1} diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.3.GCF_000007445.1.genomic.gbff --- a/test-data/genome.3.GCF_000007445.1.genomic.gbff Mon Mar 07 12:05:56 2022 +0000 +++ b/test-data/genome.3.GCF_000007445.1.genomic.gbff Wed May 04 13:15:43 2022 +0000 @@ -1,4 +1,3 @@ -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 diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.3.GCF_000007445.1.genomic.gff --- a/test-data/genome.3.GCF_000007445.1.genomic.gff Mon Mar 07 12:05:56 2022 +0000 +++ b/test-data/genome.3.GCF_000007445.1.genomic.gff Wed May 04 13:15:43 2022 +0000 @@ -1,10 +1,2 @@ -##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 c47a0a93ffd2 -r 6c829a430475 test-data/genome.3.GCF_000007445.1.seq.rpt.jsonl --- a/test-data/genome.3.GCF_000007445.1.seq.rpt.jsonl Mon Mar 07 12:05:56 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"assemblyUnit":"GCF_000007455.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2640553","genbankAccession":"AE014075.1","length":5231428,"refseqAccession":"NC_004431.1","sortOrder":1} diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.3.GCF_000013305.1.genomic.gbff --- a/test-data/genome.3.GCF_000013305.1.genomic.gbff Mon Mar 07 12:05:56 2022 +0000 +++ b/test-data/genome.3.GCF_000013305.1.genomic.gbff Wed May 04 13:15:43 2022 +0000 @@ -1,4 +1,3 @@ -LOCUS NC_008253 4938920 bp DNA circular CON 13-MAY-2021 DEFINITION Escherichia coli 536, complete sequence. ACCESSION NC_008253 VERSION NC_008253.1 diff -r c47a0a93ffd2 -r 6c829a430475 test-data/genome.3.GCF_000013305.1.genomic.gff --- a/test-data/genome.3.GCF_000013305.1.genomic.gff Mon Mar 07 12:05:56 2022 +0000 +++ b/test-data/genome.3.GCF_000013305.1.genomic.gff Wed May 04 13:15:43 2022 +0000 @@ -1,10 +1,2 @@ -##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 c47a0a93ffd2 -r 6c829a430475 test-data/genome.3.GCF_000013305.1.seq.rpt.jsonl --- a/test-data/genome.3.GCF_000013305.1.seq.rpt.jsonl Mon Mar 07 12:05:56 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"assemblyUnit":"GCF_000013315.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2495020","genbankAccession":"CP000247.1","length":4938920,"refseqAccession":"NC_008253.1","sortOrder":1}