| Previous changeset 7:0622d99c2619 (2022-06-07) Next changeset 9:18eed8fa7f23 (2022-08-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2 |
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modified:
datasets_genome.xml macros.xml |
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removed:
test-data/GCF_000001405.40.seq.rpt.jsonl |
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| diff -r 0622d99c2619 -r b2ae7186d41f datasets_genome.xml --- a/datasets_genome.xml Tue Jun 07 17:39:19 2022 +0000 +++ b/datasets_genome.xml Thu Jun 23 17:33:12 2022 +0000 |
| [ |
| @@ -35,9 +35,9 @@ --search '$filters.search_term' #end for #if $uncompressed -&& unzip ncbi_dataset.zip +&& 7z x -y ncbi_dataset.zip #else -&& unzip -l ncbi_dataset.zip > ncbi_dataset.txt +&& 7z l ncbi_dataset.zip > ncbi_dataset.txt #end if ]]></command> <inputs> @@ -233,7 +233,11 @@ <param name="uncompressed" value="true"/> <param name="released_before" value="01/02/2007"></param> <output_collection name="sequence_report"> - <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/> + <element name="GCF_000001405.40"> + <assert_contents> + <has_text text="assignedMoleculeLocationType"/> + </assert_contents> + </element> </output_collection> </test> <test expect_num_outputs="5"> @@ -260,6 +264,37 @@ </element> </output_collection> </test> + <test expect_num_outputs="3"> + <conditional name="query|subcommand"> + <param name="download_by" value="accession"></param> + <conditional name="text_or_file"> + <param name="text_or_file" value="text"></param> + <param name="accession" value="GCF_000146045.2 GCF_000002945.1"></param> + </conditional> + </conditional> + <param name="exclude_protein" value="true"/> + <param name="exclude_rna" value="true"/> + <param name="exclude_seq" value="false"/> + <param name="exclude_genomic_cds" value="true"/> + <param name="exclude_gff3" value="true"/> + <param name="uncompressed" value="true"/> + <output_collection name="genome_fasta" type="list:list" count="2"> + <element name="GCF_000146045.2"> + <element name="chrI"> + <assert_contents> + <has_text text=">NC_001133.9"/> + </assert_contents> + </element> + </element> + <element name="GCF_000002945.1"> + <element name="chrI"> + <assert_contents> + <has_text text=">NC_003424.3"/> + </assert_contents> + </element> + </element> + </output_collection> + </test> </tests> <help> <![CDATA[ |
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| diff -r 0622d99c2619 -r b2ae7186d41f macros.xml --- a/macros.xml Tue Jun 07 17:39:19 2022 +0000 +++ b/macros.xml Thu Jun 23 17:33:12 2022 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">13.21.0</token> + <token name="@TOOL_VERSION@">13.24.1</token> <token name="@PROFILE@">20.01</token> <token name="@LICENSE@">MIT</token> <token name="@VERSION_SUFFIX@">1</token> |
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| diff -r 0622d99c2619 -r b2ae7186d41f test-data/GCF_000001405.40.seq.rpt.jsonl --- a/test-data/GCF_000001405.40.seq.rpt.jsonl Tue Jun 07 17:39:19 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,191 +0,0 @@\n-{"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"}\n-{"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"}\n-{"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"}\n-{"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"}\n-{"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"}\n-{"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"}\n-{"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"}\n-{"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"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270713.1","length":40745,"refseqAccession":"NT_187368.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270713v1_random"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270714.1","length":41717,"refseqAccession":"NT_187369.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270714v1_random"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"10","gcCount":"59342366","genbankAccession":"CM000672.2","length":133797422,"refseqAccession":"NC_000010.11","role":"assembled-molecule","sortOrder":10,"ucscStyleName":"chr10"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"11","gcCount":"70204082","genbankAccession":"CM000673.2","length":135086622,"refseqAccession":"NC_000011.10","role":"assembled-molecule","sortOrder":11,"ucscStyleName":"chr11"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"12","gcCount":"58038673","genbankAccession":"CM000674.2","length":133275309,"refseqAccession":"NC_000012.12","role":"assembled-molecule","sortOrder":12,"ucscStyleName":"chr12"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"13","gcCount":"38619357","genbankAccession":"CM000675.2","length":114364328,"refseqAccession":"NC_000013.11","role":"assembled-molecule","sortOrder":13,"ucscStyleName":"chr13"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","gcCount":"45815948","genbankAccession":"CM000676.2","length":107043718,"refseqAccession":"NC_000014.9","role":"assembled-molecule","sortOrder":14,"ucscStyleName":"chr14"}\n-{"assemblyUnit":"GCF_000001305.16","assig'..b'nkAccession":"KI270745.1","length":41891,"refseqAccession":"NT_187500.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270745v1"}\n-{"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"}\n-{"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"}\n-{"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"}\n-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromos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