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annotate test-data/common-nogroup.cppipe @ 3:72a7f23f3a79 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 07:46:16 -0400
parents
children d0178bdcd00e
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3
72a7f23f3a79 "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
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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2 Version:3
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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3 DateRevision:319
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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4 GitHash:
72a7f23f3a79 "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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7
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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.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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9 :
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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14 Extract metadata?:Yes
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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15 Metadata data type:Text
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16 Metadata types:{}
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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17 Extraction method count:2
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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18 Metadata extraction method:Extract from file/folder names
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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19 Metadata source:File name
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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]+)
72a7f23f3a79 "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>.*)
72a7f23f3a79 "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
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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:
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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25 Match file and image metadata:[]
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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29 Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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30 Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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31 Extract metadata from:All images
72a7f23f3a79 "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:
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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34 Match file and image metadata:[]
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35 Use case insensitive matching?:No
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36
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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]
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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?:No
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72 grouping metadata count:1
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73 Metadata category:None