Mercurial > repos > bgruening > cp_cellprofiler
view starting_modules_metadata.xml @ 7:eb6c08714244 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | bgruening |
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date | Sun, 05 Nov 2023 09:28:09 +0000 |
parents | a98608f3abc5 |
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<macros> <xml name="image_matching_rules_metadata"> <param name="match_all_any" type="select" display="radio" label="Match the following rules"> <option value="and">All</option> <option value="or">Any</option> </param> <repeat name="r_match" title="filtering rules"> <conditional name="con_match"> <param name="rule_type" type="select" label="Select the filtering criteria"> <option value="file">File</option> <option value="directory">Directory</option> <option value="extension">Extension</option> </param> <when value="file"> <expand macro="name_type_rule_matching_file"/> </when> <when value="directory"> <expand macro="name_type_rule_matching_file"/> </when> <when value="extension"> <expand macro="name_type_rule_ext" /> </when> </conditional> </repeat> </xml> <xml name="starting_modules_metadata"> <section name="metadata" title="Metadata" expanded="false"> <conditional name="con_metadata_extraction"> <param name="extract" type="select" label="Do you want to extract the metadata?"> <option value="Yes">Yes, specify metadata</option> <option value="No" selected="true">No, do not specify metadata</option> </param> <when value="Yes"> <repeat name="extraction_method" title="new metadata" min="1"> <param name="metadata_extraction_method" type="select" label="Metadata extraction method" help="Metadata can be stored in either or both of two ways: internally (through the file naming, directory structuring, or the file header information) or externally (external index, such as spreadsheet or database of some kind). " > <option value="Extract from file/folder names">Extract from file/folder names</option> <option value="Import from file">Import from file</option> <option value="Extract from image file headers">Extract from image file headers</option> </param> <conditional name="con_metadata_source"> <param name="metadata_source" type="select" label="Metadata source" help="You can extract the metadata from the image file name or from its folder name."> <option value="File name">File name</option> <option value="Folder name">Folder name</option> </param> <when value="File name"> <param name="file_name_regex" type="select" label="Select the pattern to extract metadata from the file name" help="Image file names must comply with one of the patterns. For example, plate_reagent_timepoint.tif matches the pattern field1_field2_field3. If none of the patterns is suitable, please use other Galaxy tools to rename your files first."> <sanitizer sanitize="false"/> <option value="(?P<field1>.*)">field1</option> <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)">field1-field2</option> <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)">field1_field2</option> <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)">field1__field2</option> <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)">field1-field2-field3</option> <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)">field1_field2_field3</option> <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)">field1__field2__field3</option> <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)-(?P<field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option> <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option> <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option> <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)-(?P<field4>[a-zA-Z0-9]+)-(?P<field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option> <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)_(?P<field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option> <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)__(?P<field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option> <option value="(?P<field1>.*)-(?P<field2>[a-zA-Z0-9]+)-(?P<field3>[a-zA-Z0-9]+)-(?P<field4>[a-zA-Z0-9]+)-(?P<field5>[a-zA-Z0-9]+)-(?P<field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option> <option value="(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)_(?P<field5>[a-zA-Z0-9]+)_(?P<field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option> <option value="(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)__(?P<field5>[a-zA-Z0-9]+)__(?P<field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option> </param> </when> <when value="Folder name"> <param name="folder_name_regex" type="select" label="Select the pattern to extract metadata from the folder name" help="Folder names must comply with one of the patterns. For example, folder name exp1-channel_name matches the pattern field1-field2. If none of the patterns is suitable, please use other Galaxy tools to rename your folder first."> <sanitizer sanitize="false"/> <option value="(?P<folderField1>.*)">field1</option> <option value="(?P<folderField1>.*)-(?P<folderField2>[a-zA-Z0-9]+)">field1-field2</option> <option value="(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)">field1_field2</option> </param> </when> </conditional> <conditional name="con_metadata_extract_from"> <param name="extract_metadata_from" type="select" label="Extract metadata from"> <option value="All images">All images</option> <option value="Images matching a rule">Images matching a rule</option> </param> <when value="Images matching a rule"> <expand macro="image_matching_rules_metadata" /> </when> <when value="All images" /> </conditional> </repeat> </when> <when value="No" /> </conditional> </section> </xml> </macros>