# HG changeset patch # User iuc # Date 1753126096 0 # Node ID 0f3b3813b6aef17440d0252b681c9a1096417125 # Parent 7b925f7c50b2d8232de647b3380c71caed41f364 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c1c3f90e4aa7dc258aa61d98ec4eac0b97eef426 diff -r 7b925f7c50b2 -r 0f3b3813b6ae datasets_gene.xml --- a/datasets_gene.xml Mon Mar 17 11:05:45 2025 +0000 +++ b/datasets_gene.xml Mon Jul 21 19:28:16 2025 +0000 @@ -4,7 +4,7 @@ macros.xml - + - - + + @@ -109,8 +109,8 @@ - - + + @@ -133,7 +133,7 @@ - + @@ -235,12 +235,12 @@ - + - + @@ -263,12 +263,12 @@ - + - + @@ -284,6 +284,7 @@
+
@@ -297,17 +298,17 @@ - + - + - + @@ -315,11 +316,6 @@ -
- - - -
@@ -361,17 +357,17 @@ - + - +
- + @@ -380,11 +376,6 @@ -
- - - -
@@ -395,7 +386,7 @@
- + @@ -403,11 +394,6 @@ -
- - - -
@@ -417,7 +403,7 @@
- + @@ -426,11 +412,6 @@ -
- - - -
@@ -439,7 +420,6 @@
- @@ -466,24 +446,23 @@ - + - + - + - - +
@@ -184,19 +190,19 @@ - + - + - + - + @@ -214,26 +220,27 @@ - - - +
+ + + +
- - - - - - - - - - - - - + + + + + + + + + + + + @@ -365,8 +377,10 @@ - - +
+ + +
@@ -395,19 +409,19 @@ - + - + - + @@ -437,7 +451,7 @@ - + @@ -463,22 +477,21 @@ - - + +
- + - - + diff -r 7b925f7c50b2 -r 0f3b3813b6ae macros.xml --- a/macros.xml Mon Mar 17 11:05:45 2025 +0000 +++ b/macros.xml Mon Jul 21 19:28:16 2025 +0000 @@ -1,5 +1,5 @@ - 17.1.0 + 18.4.1 0 23.0 MIT @@ -12,7 +12,8 @@ ncbi-datasets-cli ca-certificates - unzip + + diff -r 7b925f7c50b2 -r 0f3b3813b6ae test-data/GCF_000007445.1.genomic.gtf --- a/test-data/GCF_000007445.1.genomic.gtf Mon Mar 17 11:05:45 2025 +0000 +++ b/test-data/GCF_000007445.1.genomic.gtf Mon Jul 21 19:28:16 2025 +0000 @@ -1,6 +1,5 @@ -#!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 Protein Homology CDS 190 252 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; +NC_004431.1 Protein Homology start_codon 190 192 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; +NC_004431.1 Protein Homology stop_codon 253 255 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 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 7b925f7c50b2 -r 0f3b3813b6ae test-data/genome.2.GCF_000013305.1.genomic.gtf --- a/test-data/genome.2.GCF_000013305.1.genomic.gtf Mon Mar 17 11:05:45 2025 +0000 +++ b/test-data/genome.2.GCF_000013305.1.genomic.gtf Mon Jul 21 19:28:16 2025 +0000 @@ -1,6 +1,5 @@ -#!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 Protein Homology CDS 190 252 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; +NC_008253.1 Protein Homology start_codon 190 192 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; +NC_008253.1 Protein Homology stop_codon 253 255 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 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";