| Previous changeset 14:75acf92c8fd5 (2023-09-21) Next changeset 16:a6a475ed58cb (2024-06-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a |
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modified:
datasets_gene.xml datasets_genome.xml macros.xml |
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| diff -r 75acf92c8fd5 -r 198c75abbf55 datasets_gene.xml --- a/datasets_gene.xml Thu Sep 21 23:02:58 2023 +0000 +++ b/datasets_gene.xml Mon Mar 04 17:27:59 2024 +0000 |
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| @@ -391,7 +391,6 @@ </assert_contents> </output> </test> - <!-- 7: datasets download gene accession NP_000483.3 --> <test expect_num_outputs="1"> <conditional name="query|subcommand"> @@ -438,8 +437,10 @@ </output> </test> - <!-- 9: datasets download gene accession WP_004675351.1 + include_flanks_bp --> - <test expect_num_outputs="3"> + <!-- 9: datasets download gene accession WP_004675351.1 + include_flanks_bp + test broken at the moment https://github.com/ncbi/datasets/issues/328 + --> + <test expect_failure="true"> <!-- expect_num_outputs="3" --> <conditional name="query|subcommand"> <param name="download_by" value="accession"/> <conditional name="text_or_file"> @@ -454,7 +455,7 @@ <param name="include" value="gene,protein"/> </conditional> </section> - <output name="gene_data_report"> + <!-- <output name="gene_data_report"> <assert_contents> <has_text text="glcE"/> <has_n_lines n="2"/> @@ -470,7 +471,7 @@ <assert_contents> <has_text text=">"/> </assert_contents> - </output> + </output> --> <assert_command> <has_text text="include-flanks-bp 100"/> </assert_command> |
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| diff -r 75acf92c8fd5 -r 198c75abbf55 datasets_genome.xml --- a/datasets_genome.xml Thu Sep 21 23:02:58 2023 +0000 +++ b/datasets_genome.xml Mon Mar 04 17:27:59 2024 +0000 |
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| @@ -33,6 +33,10 @@ --chromosomes '$filters.chromosomes' #end if $filters.exclude_atypical +#if $filters.mag: + --mag '$filters.mag' +#end if + @INCLUDE@ @RELEASED_BEFORE@ @RELEASED_AFTER@ @@ -106,6 +110,10 @@ <expand macro="assembly_source"/> <expand macro="chromosomes"/> <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/> + <param argument="--mag" type="select" multiple="false" optional="true" label="Filter metagenome assembled genomes (MAGs)"> + <option value="only" selected="false">Limit to MAGs</option> + <option value="exclude" selected="false">Exclude MAGs</option> + </param> <expand macro="released_options"/> <expand macro="released_options" before_or_after="after"/> @@ -332,8 +340,8 @@ </section> <output name="genome_data_report"> <assert_contents> - <has_text text="GCF_000013305.1"/> - <has_text text="GCF_000007445.1"/> + <has_text text="GCF_000013305.1"/> + <has_text text="GCF_000007445.1"/> <has_n_lines n="3"/> <has_n_columns n="4"/> </assert_contents> @@ -349,7 +357,7 @@ </test> <!-- should not fail https://github.com/ncbi/datasets/issues/194 --> - <test expect_num_outputs="2"> <!-- expect_failure="true"> --> + <test expect_num_outputs="2"> <conditional name="query|subcommand"> <param name="download_by" value="accession"/> <conditional name="text_or_file"> @@ -362,9 +370,17 @@ <section name="file_choices"> <param name="include" value="seq-report"/> </section> - <!-- - <output_collection name="sequence_report" type="list" count="4" > - --> + <output name="genome_data_report"> + <!-- assert that we get at least the 16 versions available at the time of writing this test --> + <assert_contents> + <has_text text="GCF_000001405" min="16"/> + <has_n_lines min="16"/> + <has_n_columns n="4"/> + </assert_contents> + </output> + <!--not testing the collection output. the count will change over time + and this can't be tested for at the moment + <output_collection name="sequence_report" type="list" count="16"/> --> </test> <test expect_num_outputs="5"> <conditional name="query|subcommand"> @@ -413,7 +429,7 @@ <element name="GCF_000146045.2"> <element name="GCF_000146045.2_R64" ftype="fasta.gz"> <assert_contents> - <has_size value="3843460"/> + <has_size value="3843460" delta="2000"/> </assert_contents> </element> </element> @@ -421,14 +437,14 @@ <output_collection name="protein_fasta" type="list" count="1"> <element name="GCF_000146045.2" ftype="fasta.gz"> <assert_contents> - <has_size value="1845038"/> + <has_size value="1845038" delta="2000"/> </assert_contents> </element> </output_collection> <output_collection name="rna_fasta" type="list" count="1"> <element name="GCF_000146045.2" ftype="fasta.gz"> <assert_contents> - <has_size value="2784899"/> + <has_size value="2784899" delta="2000"/> </assert_contents> </element> </output_collection> @@ -451,10 +467,9 @@ <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/> </output_collection> </test> - <!-- tax_exact_match seems not able to filter out strains - https://github.com/ncbi/datasets/issues/187 - hence we set expect_test_failure="true"--> - <test expect_num_outputs="1" expect_test_failure="true"> + <!-- tax_exact_match should filter out strains + https://github.com/ncbi/datasets/issues/187 --> + <test expect_num_outputs="1"> <conditional name="query|subcommand"> <param name="download_by" value="taxon"/> <param name="taxon_positional" value="4932"/> |
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| diff -r 75acf92c8fd5 -r 198c75abbf55 macros.xml --- a/macros.xml Thu Sep 21 23:02:58 2023 +0000 +++ b/macros.xml Mon Mar 04 17:27:59 2024 +0000 |
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| @@ -1,17 +1,17 @@ <macros> - <token name="@TOOL_VERSION@">15.19.1</token> + <token name="@TOOL_VERSION@">16.6.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <token name="@LICENSE@">MIT</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 +## If running in a container use certificates from ca-certificates instead of outdated/missing container certificates [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem"; ]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement> - <requirement type="package" version="2023.7.22">ca-certificates</requirement> + <requirement type="package" version="2024.2.2">ca-certificates</requirement> <requirement type="package" version="16.02">p7zip</requirement> </requirements> </xml> @@ -71,7 +71,7 @@ </xml> <xml name="taxon_positional"> - <param name="taxon_positional" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."/> + <param name="taxon_positional" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc. or use Taxonomy ID from NCBI for greater accuracy, use species-level only not genera or larger taxa"/> </xml> <xml name="ortholog"> |