annotate test-data/color_to_gray_combine_channels.cppipe @ 6:f24c370e5ea4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:35:54 +0000
parents d0178bdcd00e
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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:
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5 ModuleCount:5
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6 HasImagePlaneDetails:False
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7
5
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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
5
d0178bdcd00e "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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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:1
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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]+)
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21 Regular expression to extract from folder name:(?P<folderField1>.*)
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22 Extract metadata from:All images
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23 Select the filtering criteria:and (file does contain "")
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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
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28 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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29 Assign a name to:Images matching rules
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30 Select the image type:Grayscale image
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31 Name to assign these images:DNA
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32 Match metadata:[]
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33 Image set matching method:Order
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34 Set intensity range from:Image metadata
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35 Assignments count:1
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36 Single images count:0
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37 Maximum intensity:255.0
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38 Process as 3D?:No
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39 Relative pixel spacing in X:1.0
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40 Relative pixel spacing in Y:1.0
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41 Relative pixel spacing in Z:1.0
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42 Select the rule criteria:and (file does startwith "im")
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43 Name to assign these images:DNA
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44 Name to assign these objects:Cell
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45 Select the image type:Grayscale image
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46 Set intensity range from:Image metadata
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47 Select the image type:Grayscale image
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48 Maximum intensity:255.0
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49
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50 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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51 Do you want to group your images?:Yes
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52 grouping metadata count:1
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53 Metadata category:field1
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54
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55 ColorToGray:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Convert the color image to grayscale.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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56 Select the input image:DNA
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57 Conversion method:Combine
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58 Image type:Channels
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59 Name the output image:OrigGray
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60 Relative weight of the red channel:1.0
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61 Relative weight of the green channel:1.0
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62 Relative weight of the blue channel:1.0
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63 Convert red to gray?:Yes
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64 Name the output image:OrigRed
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65 Convert green to gray?:Yes
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66 Name the output image:OrigGreen
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67 Convert blue to gray?:Yes
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68 Name the output image:OrigBlue
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69 Convert hue to gray?:Yes
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70 Name the output image:OrigHue
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71 Convert saturation to gray?:Yes
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72 Name the output image:OrigSaturation
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73 Convert value to gray?:Yes
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74 Name the output image:OrigValue
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75 Channel count:2
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76 Channel number:2
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77 Relative weight of the channel:0.2
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78 Image name:Channel1
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79 Channel number:3
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80 Relative weight of the channel:0.5
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81 Image name:Channel1