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73 lines
4.0 KiB
XML
73 lines
4.0 KiB
XML
<tool id="export_remote" name="Export datasets" version="0.1.0" profile="21.05">
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<description>to remote files source</description>
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<!-- TODO
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<requirements>
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<requirement type="package" version="21.05">galaxy-files</requirement>
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</requirements>
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-->
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<command><![CDATA[
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python '$__tool_directory__/export_remote.py'
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--file-sources '$file_sources'
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--directory-uri '$d_uri'
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--files-to-export '$files_to_export'
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--export-metadata-files $include_metadata_files
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> '$out'
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]]></command>
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<configfiles>
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<file_sources name="file_sources" />
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<configfile name="files_to_export">#import json
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#from galaxy.util import filesystem_safe_string
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#if $export_type.export_type_selector == "datasets_auto":
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#set $fileconfig = json.dumps($export_type.infiles.serialize(invalid_chars=tuple(str($invalid_chars))))
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#else if $export_type.export_type_selector == "collection_auto":
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#set $fileconfig = json.dumps($export_type.incollection.serialize(invalid_chars=tuple(str($invalid_chars)), include_collection_name=bool($export_type.include_collection_name)))
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#else
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#set $fileconfig = [d['infile'].serialize() for d in $export_type.datasets]
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#for $i, $dataset in enumerate($export_type.datasets):
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#silent $fileconfig[$i]['staging_path'] = filesystem_safe_string(str(dataset["name"]), 255, invalid_chars=())
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#end for
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#silent fileconfig = json.dumps($fileconfig)
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#end if
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$fileconfig
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</configfile>
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</configfiles>
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<inputs>
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<conditional name="export_type">
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<param name="export_type_selector" type="select" label="What would you like to export?">
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<option value="datasets_auto" selected="true">Datasets using their Galaxy name and extension</option>
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<option value="collection_auto">Dataset Collection using their name, structure and extension</option>
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<option value="datasets_named">Datasets specifying their names</option>
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<!-- Allow more options - e.g. HTML, collections preserving their structure... -->
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</param>
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<when value="datasets_auto">
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<param name="infiles" type="data" format="data" multiple="true" label="Choose your datasets" help="Datasets must have unique names"/>
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</when>
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<when value="collection_auto">
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<param name="incollection" type="data_collection" format="data" label="Choose your dataset collection" help="Dataset collection will be exported. Collections will become folders and datasets will be files"/>
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<param name="include_collection_name" type="boolean" label="Include the collection name as top level directory?"/>
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</when>
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<when value="datasets_named">
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<repeat name="datasets" title="Dataset">
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<param type="data" format="data" name="infile" label="Input dataset" />
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<param type="text" name="name" label="Enter file name" help="To create a file named "f1.txt" in directory named "dir1" enter "dir1/f1.txt"">
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<!-- 🔥 turn off sanitizer, so unicode strings can be used. Is sanitized in configfile -->
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<sanitizer sanitize="false"></sanitizer>
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<validator type="length" min="1" max="255"/>
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</param>
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</repeat>
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</when>
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</conditional>
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<param type="directory_uri" name="d_uri" label="Directory URI" />
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<param name="include_metadata_files" type="boolean" checked="true" label="Include metadata files in export?" help="Examples of metadata files are bam, cram and vcf indexes that can be regenerated from raw data" />
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<param name="invalid_chars" type="select" label="Select which characters should be stripped from the exported paths">
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<option value="/">Sanitize /</option>
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<option value="">Don't sanitize values</option>
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</param>
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</inputs>
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<outputs>
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<data name="out" format="txt" label="Export logs"/>
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</outputs>
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<tests>
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</tests>
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</tool>
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