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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:26:46 +0000
parents 6a7da2e5f696
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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1 CellProfiler Pipeline: http://www.cellprofiler.org
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2 Version:3
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3 DateRevision:319
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4 GitHash:
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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5 ModuleCount:4
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6 HasImagePlaneDetails:False
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8 Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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9 :
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10 Filter images?:Images only
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11 Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
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12
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6a7da2e5f696 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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13 Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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14 Extract metadata?:Yes
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15 Metadata data type:Text
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16 Metadata types:{}
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17 Extraction method count:2
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18 Metadata extraction method:Extract from file/folder names
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19 Metadata source:File name
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20 Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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21 Regular expression to extract from folder name:(?P<folderField1>.*)
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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22 Extract metadata from:Images matching a rule
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23 Select the filtering criteria:and (file does contain "im") (extension does istif)
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24 Metadata file location:
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25 Match file and image metadata:[]
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26 Use case insensitive matching?:No
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27 Metadata extraction method:Extract from file/folder names
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28 Metadata source:Folder name
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29 Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
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30 Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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31 Extract metadata from:All images
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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32 Select the filtering criteria:and (file does contain "")
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33 Metadata file location:
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34 Match file and image metadata:[]
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35 Use case insensitive matching?:No
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37 NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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38 Assign a name to:Images matching rules
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39 Select the image type:Grayscale image
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40 Name to assign these images:DNA
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41 Match metadata:[]
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42 Image set matching method:Order
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43 Set intensity range from:Image metadata
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44 Assignments count:3
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45 Single images count:0
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46 Maximum intensity:255.0
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47 Process as 3D?:No
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48 Relative pixel spacing in X:1.0
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49 Relative pixel spacing in Y:1.0
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50 Relative pixel spacing in Z:1.0
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51 Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
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52 Name to assign these images:DNA
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53 Name to assign these objects:Cell
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54 Select the image type:Objects
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55 Set intensity range from:Image metadata
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56 Maximum intensity:255.0
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57 Select the rule criteria:and (file does contain "")
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58 Name to assign these images:GFP
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59 Name to assign these objects:Cell
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60 Select the image type:Illumination function
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61 Set intensity range from:Image metadata
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62 Maximum intensity:255.0
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63 Select the rule criteria:or (extension does istif)
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64 Name to assign these images:Actin
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65 Name to assign these objects:Cell
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66 Select the image type:Grayscale image
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67 Set intensity range from:Image metadata
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68 Maximum intensity:255.0
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69
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70 Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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71 Do you want to group your images?:Yes
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72 grouping metadata count:1
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73 Metadata category:field1