| Previous changeset 6:5a2656cc84cb (2022-06-06) Next changeset 8:b2ae7186d41f (2022-06-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 7fc0becfda6c41c95d4aa9ee32ae0539be9b6210 |
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modified:
datasets_genome.xml macros.xml |
| b |
| diff -r 5a2656cc84cb -r 0622d99c2619 datasets_genome.xml --- a/datasets_genome.xml Mon Jun 06 13:41:05 2022 +0000 +++ b/datasets_genome.xml Tue Jun 07 17:39:19 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@"> +<tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>download genome sequence, annotation and metadata</description> <macros> <import>macros.xml</import> @@ -89,7 +89,7 @@ <filter>uncompressed</filter> </collection> <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list"> - <discover_datasets pattern="(?P<identifier_0>.*?)\/(?P<identifier_1>.*?)\.(?<!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> + <discover_datasets pattern="(?P<identifier_0>.*?)\/(?!rna|cds_from)(?P<identifier_1>.*?)\.(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> <filter>uncompressed and not file_choices['exclude_seq']</filter> </collection> <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list"> @@ -236,7 +236,7 @@ <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/> </output_collection> </test> - <test expect_num_outputs="3"> + <test expect_num_outputs="5"> <conditional name="query|subcommand"> <param name="download_by" value="accession"></param> <conditional name="text_or_file"> @@ -245,9 +245,9 @@ </conditional> </conditional> <param name="exclude_protein" value="true"/> - <param name="exclude_rna" value="true"/> + <param name="exclude_rna" value="false"/> <param name="exclude_seq" value="false"/> - <param name="exclude_genomic_cds" value="true"/> + <param name="exclude_genomic_cds" value="false"/> <param name="exclude_gff3" value="true"/> <param name="uncompressed" value="true"/> <output_collection name="genome_fasta" type="list:list" count="1"> |
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| diff -r 5a2656cc84cb -r 0622d99c2619 macros.xml --- a/macros.xml Mon Jun 06 13:41:05 2022 +0000 +++ b/macros.xml Tue Jun 07 17:39:19 2022 +0000 |
| [ |
| @@ -2,6 +2,7 @@ <token name="@TOOL_VERSION@">13.21.0</token> <token name="@PROFILE@">20.01</token> <token name="@LICENSE@">MIT</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token> <token name="@SETUP_CERTIFICATES@"><![CDATA[ ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates |