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mvdbeek
32 lines
1.5 KiB
XML
32 lines
1.5 KiB
XML
<tool name="NCBI Datasets Genomes" id="ncbi_datasets_source" tool_type="data_source" version="@TOOL_VERSION@" profile="21.09">
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<description>import data from the NCBI Datasets Genomes page</description>
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<edam_operations>
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<edam_operation>operation_0224</edam_operation>
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</edam_operations>
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<macros>
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<token name="@TOOL_VERSION@">13.14.0</token>
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</macros>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
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</requirements>
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<version_command>datasets version</version_command>
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<command><![CDATA[
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## If running in container use certificate from ca-certificates instead of outdated / missing container certificates
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[ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
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datasets download --input-json '$file_param' --filename '$compressed_archive' --no-progressbar
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&& unzip -l '$compressed_archive'
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]]></command>
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<inputs action="https://www.ncbi.nlm.nih.gov/datasets/genomes" check_values="true" method="get">
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<display>go to NCBI Datasets Genomes server $GALAXY_URL</display>
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<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ncbi_datasets_source"/>
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<param name="file_param" type="file"/>
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</inputs>
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<outputs>
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<data name="compressed_archive" format="ncbi_genome_dataset.zip" label="NCBI Genome Dataset"/>
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</outputs>
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<options sanitize="true"/>
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<citations>
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<citation type="doi">10.1093/database/bar011</citation>
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</citations>
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</tool>
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