Mercurial > repos > bgruening > cp_identify_primary_objects

comparison starting_modules_metadata.xml @ 3:52c01fb29b2a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:48:09 -0400
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2:d9bf32d13dfd 3:52c01fb29b2a
1 <macros>
2 <xml name="image_matching_rules_metadata">
3 <param name="match_all_any" type="select" display="radio" label="Match the following rules">
4 <option value="and">All</option>
5 <option value="or">Any</option>
6 </param>
7 <repeat name="r_match" title="filtering rules">
8 <conditional name="con_match">
9 <param name="rule_type" type="select" label="Select the filtering criteria">
10 <option value="file">File</option>
11 <option value="directory">Directory</option>
12 <option value="extension">Extension</option>
13 </param>
14 <when value="file">
15 <expand macro="name_type_rule_matching_file"/>
16 </when>
17 <when value="directory">
18 <expand macro="name_type_rule_matching_file"/>
19 </when>
20 <when value="extension">
21 <expand macro="name_type_rule_ext" />
22 </when>
23 </conditional>
24 </repeat>
25 </xml>
26 <xml name="starting_modules_metadata">
27 <section name="metadata" title="Metadata" expanded="false">
28 <conditional name="con_metadata_extraction">
29 <param name="extract" type="select" label="Do you want to extract the metadata?">
30 <option value="Yes">Yes, specify metadata</option>
31 <option value="No" selected="true">No, do not specify metadata</option>
32 </param>
33 <when value="Yes">
34 <repeat name="extraction_method" title="new metadata" min="1">
35 <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). " >
36 <option value="Extract from file/folder names">Extract from file/folder names</option>
37 <option value="Import from file">Import from file</option>
38 <option value="Extract from image file headers">Extract from image file headers</option>
39 </param>
40 <conditional name="con_metadata_source">
41 <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.">
42 <option value="File name">File name</option>
43 <option value="Folder name">Folder name</option>
44 </param>
45 <when value="File name">
46 <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.">
47
48 <sanitizer sanitize="false"/>
49 <option value="(?P&lt;field1>.*)">field1</option>
50 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
51 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
52 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
53 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
54 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
55 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
56 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option>
57 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option>
58 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option>
59 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option>
60 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option>
61 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
62 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
63 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
64 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
65 </param>
66 </when>
67 <when value="Folder name">
68 <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.">
69 <sanitizer sanitize="false"/>
70 <option value="(?P&lt;folderField1>.*)">field1</option>
71 <option value="(?P&lt;folderField1>.*)-(?P&lt;folderField2>[a-zA-Z0-9]+)">field1-field2</option>
72 <option value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)">field1_field2</option>
73 </param>
74 </when>
75 </conditional>
76 <conditional name="con_metadata_extract_from">
77 <param name="extract_metadata_from" type="select" label="Extract metadata from">
78 <option value="All images">All images</option>
79 <option value="Images matching a rule">Images matching a rule</option>
80 </param>
81 <when value="Images matching a rule">
82 <expand macro="image_matching_rules_metadata" />
83 </when>
84 <when value="All images" />
85 </conditional>
86 </repeat>
87 </when>
88 <when value="No" />
89 </conditional>
90 </section>
91 </xml>
92 </macros>