Mercurial > repos > iuc > ncbi_datasets
changeset 14:75acf92c8fd5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
| author | iuc |
|---|---|
| date | Thu, 21 Sep 2023 23:02:58 +0000 |
| parents | 1e188c9610c3 |
| children | 198c75abbf55 |
| files | datasets_gene.xml datasets_genome.xml macros.xml |
| diffstat | 3 files changed, 27 insertions(+), 27 deletions(-) [+] |
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--- a/datasets_gene.xml Fri Dec 09 15:11:16 2022 +0000 +++ b/datasets_gene.xml Thu Sep 21 23:02:58 2023 +0000 @@ -422,7 +422,7 @@ <param name="text_or_file" value="text"/> <param name="accession" value="NM_000546.6 NM_000492.4"/> </conditional> - <param name="ortholog" value="true"/> + <param name="ortholog" value="all"/> </conditional> <section name="file_choices"> <conditional name="kingdom_cond">
--- a/datasets_genome.xml Fri Dec 09 15:11:16 2022 +0000 +++ b/datasets_genome.xml Thu Sep 21 23:02:58 2023 +0000 @@ -162,14 +162,6 @@ </collection> </outputs> <tests> - <!-- Note: All but one test use the non-default decompress="true" - - this is because (at 11/22) Galaxy can not apply text assertions on the content - of compressed files https://github.com/galaxyproject/galaxy/pull/15085 - - So with decompress="true" more powerfull assertions are powerful. - A single test checks the default, ie decompress="false". - --> <test expect_num_outputs="3"> <conditional name="query|subcommand"> <param name="download_by" value="taxon"/> @@ -185,7 +177,7 @@ <output name="genome_data_report"> <assert_contents> <has_text text="Assembly Accession	Assembly Name	Assembly Submitter	Organism Name"/> - <has_n_lines n="144"/> + <has_n_lines n="142"/> <has_n_columns n="4"/> </assert_contents> </output> @@ -201,8 +193,7 @@ <assert_contents> <has_n_lines min="1000000"/> <has_line line="##gff-version 3"/> - <!-- TODO this will only work when the galaxy python packakes for 22.05 have been released - <has_n_columns n="9" comment="#"/> --> + <has_n_columns n="9" comment="#"/> </assert_contents> </element> </output_collection> @@ -222,22 +213,24 @@ <param name="include" value="genome"/> <param name="decompress" value="true"/> </section> - <output_collection name="genome_fasta" type="list:list" count="14"> + <output_collection name="genome_fasta" type="list:list" count="12"> <expand macro="genome_fasta_assert" el1="GCA_000002115.2" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_000002125.2" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_000002135.3" el2="GCA_000002135.3_CRA_TCAGchr7v2" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_000212995.1" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_000252825.1" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_000306695.2" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_000365445.1" el2="chr21" expression=">"/> - <!-- TODO chromosomes argument (or data) seems not reliable https://github.com/ncbi/datasets/issues/188--> - <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/> <expand macro="genome_fasta_assert" el1="GCA_001292825.2" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_001524155.4" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_001712695.1" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCA_022833125.2" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/> + <!-- According to https://github.com/ncbi/datasets/issues/188, the following should not be included among the returned results anymore 09/2023 --> + <!-- + <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/> + <expand macro="genome_fasta_assert" el1="GCA_000002135.3" el2="GCA_000002135.3_CRA_TCAGchr7v2" expression=">"/> + --> </output_collection> <output name="genome_data_report"> <assert_contents> @@ -246,8 +239,8 @@ </assert_contents> </output> </test> - <!-- same as previous test but assembly_source (refseq which removes some of the genomes) --> - <test expect_num_outputs="2"> + <!-- same as previous test but assembly_source=refseq, which removes all of the genomes --> + <test expect_failure="true"> <conditional name="query|subcommand"> <param name="download_by" value="taxon"/> <param name="taxon_positional" value="human"/> @@ -260,6 +253,13 @@ <param name="include" value="genome"/> <param name="decompress" value="true"/> </section> + <assert_stderr> + <has_text text="No assemblies found that match selection"/> + </assert_stderr> + <!-- In the current state of the NCBI tool/DB, no output to check. + But the returned results seem to change from time to time and it might + be necessary to re-enable this code block if the test fails in the future. --> + <!-- <output_collection name="genome_fasta" type="list:list" count="2"> <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/> <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/> @@ -270,7 +270,7 @@ <has_n_lines n="5"/> <has_n_columns n="4"/> </assert_contents> - </output> + </output> --> </test> <test expect_num_outputs="4"> <conditional name="query|subcommand"> @@ -313,8 +313,8 @@ <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/> </output_collection> <output_collection name="genomic_cds" type="list"> - <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains" decompress="true"/> - <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains" decompress="true"/> + <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/> + <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/> </output_collection> </test> <test expect_num_outputs="4"> @@ -349,7 +349,7 @@ </test> <!-- should not fail https://github.com/ncbi/datasets/issues/194 --> - <test expect_num_outputs="2" expect_failure="true"> + <test expect_num_outputs="2"> <!-- expect_failure="true"> --> <conditional name="query|subcommand"> <param name="download_by" value="accession"/> <conditional name="text_or_file"> @@ -421,14 +421,14 @@ <output_collection name="protein_fasta" type="list" count="1"> <element name="GCF_000146045.2" ftype="fasta.gz"> <assert_contents> - <has_size value="1844838"/> + <has_size value="1845038"/> </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="2784534"/> + <has_size value="2784899"/> </assert_contents> </element> </output_collection>
--- a/macros.xml Fri Dec 09 15:11:16 2022 +0000 +++ b/macros.xml Thu Sep 21 23:02:58 2023 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">14.6.0</token> + <token name="@TOOL_VERSION@">15.19.1</token> <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">21.01</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[ @@ -11,7 +11,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement> - <requirement type="package" version="2022.9.24">ca-certificates</requirement> + <requirement type="package" version="2023.7.22">ca-certificates</requirement> <requirement type="package" version="16.02">p7zip</requirement> </requirements> </xml>