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[24.1] Fix export_remote include/exclude metadata flag #18659

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Aug 8, 2024
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[24.1] Fix export_remote include/exclude metadata flag #18659

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2 changes: 1 addition & 1 deletion tools/data_export/export_remote.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def _parser():
parser.add_argument("--directory-uri", type=str, help="directory target URI")
parser.add_argument("--file-sources", type=str, help="file sources json")
parser.add_argument("--files-to-export", type=str, help="files to export")
parser.add_argument("--export-metadata-files", type=bool, help="export metadata files", default=True)
parser.add_argument("--export-metadata-files", type=bool, help="export metadata files", default=False)
return parser


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14 changes: 8 additions & 6 deletions tools/data_export/export_remote.xml
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Expand Up @@ -10,11 +10,13 @@ python '$__tool_directory__/export_remote.py'
--file-sources '$file_sources'
--directory-uri '$d_uri'
--files-to-export '$files_to_export'
--export-metadata-files $include_metadata_files
#if $include_metadata_files:
--export-metadata-files $include_metadata_files
#end if
> '$out'
]]></command>
<configfiles>
<file_sources name="file_sources" />
<file_sources name="file_sources"/>
<configfile name="files_to_export">#import json
#from galaxy.util import filesystem_safe_string
#if $export_type.export_type_selector == "datasets_auto":
Expand Down Expand Up @@ -48,17 +50,17 @@ $fileconfig
</when>
<when value="datasets_named">
<repeat name="datasets" title="Dataset">
<param type="data" format="data" name="infile" label="Input dataset" />
<param type="data" format="data" name="infile" label="Input dataset"/>
<param type="text" name="name" label="Enter file name" help="To create a file named &quot;f1.txt&quot; in directory named &quot;dir1&quot; enter &quot;dir1/f1.txt&quot;">
<!-- 🔥 turn off sanitizer, so unicode strings can be used. Is sanitized in configfile -->
<sanitizer sanitize="false"></sanitizer>
<sanitizer sanitize="false"/>
<validator type="length" min="1" max="255"/>
</param>
</repeat>
</when>
</conditional>
<param type="directory_uri" name="d_uri" label="Directory URI" />
<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" />
<param type="directory_uri" name="d_uri" label="Directory URI"/>
<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"/>
<param name="invalid_chars" type="select" label="Select which characters should be stripped from the exported paths">
<option value="/">Sanitize /</option>
<option value="">Don't sanitize values</option>
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