Mercurial > repos > bgruening > cp_save_images

annotate starting_modules_metadata.xml @ 3:a45d360ae9d9 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 07:51:22 -0400
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3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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1 <macros>
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2 <xml name="image_matching_rules_metadata">
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3 <param name="match_all_any" type="select" display="radio" label="Match the following rules">
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4 <option value="and">All</option>
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5 <option value="or">Any</option>
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6 </param>
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7 <repeat name="r_match" title="filtering rules">
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8 <conditional name="con_match">
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9 <param name="rule_type" type="select" label="Select the filtering criteria">
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10 <option value="file">File</option>
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11 <option value="directory">Directory</option>
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12 <option value="extension">Extension</option>
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13 </param>
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14 <when value="file">
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15 <expand macro="name_type_rule_matching_file"/>
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16 </when>
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17 <when value="directory">
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18 <expand macro="name_type_rule_matching_file"/>
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19 </when>
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20 <when value="extension">
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21 <expand macro="name_type_rule_ext" />
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22 </when>
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23 </conditional>
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24 </repeat>
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25 </xml>
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26 <xml name="starting_modules_metadata">
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27 <section name="metadata" title="Metadata" expanded="false">
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28 <conditional name="con_metadata_extraction">
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29 <param name="extract" type="select" label="Do you want to extract the metadata?">
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30 <option value="Yes">Yes, specify metadata</option>
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31 <option value="No" selected="true">No, do not specify metadata</option>
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32 </param>
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33 <when value="Yes">
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34 <repeat name="extraction_method" title="new metadata" min="1">
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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). " >
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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36 <option value="Extract from file/folder names">Extract from file/folder names</option>
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37 <option value="Import from file">Import from file</option>
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38 <option value="Extract from image file headers">Extract from image file headers</option>
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39 </param>
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40 <conditional name="con_metadata_source">
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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.">
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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42 <option value="File name">File name</option>
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43 <option value="Folder name">Folder name</option>
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44 </param>
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45 <when value="File name">
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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.">
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47
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48 <sanitizer sanitize="false"/>
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49 <option value="(?P&lt;field1>.*)">field1</option>
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50 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
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51 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
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52 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
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53 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
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54 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
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55 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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65 </param>
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66 </when>
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67 <when value="Folder name">
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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.">
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69 <sanitizer sanitize="false"/>
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70 <option value="(?P&lt;folderField1>.*)">field1</option>
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71 <option value="(?P&lt;folderField1>.*)-(?P&lt;folderField2>[a-zA-Z0-9]+)">field1-field2</option>
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72 <option value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)">field1_field2</option>
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73 </param>
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74 </when>
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75 </conditional>
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76 <conditional name="con_metadata_extract_from">
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77 <param name="extract_metadata_from" type="select" label="Extract metadata from">
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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78 <option value="All images">All images</option>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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79 <option value="Images matching a rule">Images matching a rule</option>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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80 </param>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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81 <when value="Images matching a rule">
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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82 <expand macro="image_matching_rules_metadata" />
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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83 </when>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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84 <when value="All images" />
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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85 </conditional>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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86 </repeat>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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87 </when>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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88 <when value="No" />
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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89 </conditional>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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90 </section>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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91 </xml>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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92 </macros>