Merge pull request #18659 from davelopez/fix_remote_export_tool_exclu…

…de_metadata [24.1] Fix export_remote include/exclude metadata flag
galaxyproject · Aug 8, 2024 · e059a16 · e059a16
2 parents 2a670b4 + 7d00202
commit e059a16
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/tools/data_export/export_remote.py b/tools/data_export/export_remote.py
@@ -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
 
 

diff --git a/tools/data_export/export_remote.xml b/tools/data_export/export_remote.xml
@@ -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":
@@ -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>