annotate test-data/measure_image_intensity.txt @ 2:b6f13e783ac5 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author bgruening
date Thu, 16 Apr 2020 05:43:08 -0400
parents f9969a97f034
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3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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:
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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5 ModuleCount:5
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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.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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9 :
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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 ".")
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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12
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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]
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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14 Extract metadata?:Yes
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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15 Metadata data type:Text
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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16 Metadata types:{}
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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17 Extraction method count:1
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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18 Metadata extraction method:Extract from file/folder names
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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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f9969a97f034 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6a3036d24b5ec074936f8f8283b7e176f6f1ce70"
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21 Regular expression to extract from folder name:(?P<field1>.*)
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22 Extract metadata from:All images
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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23 Select the filtering criteria:and (file does contain "")
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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24 Metadata file location:
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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25 Match file and image metadata:[]
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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26 Use case insensitive matching?:No
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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]
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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29 Assign a name to:Images matching rules
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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30 Select the image type:Grayscale image
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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31 Name to assign these images:DNA
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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
3a2cfcd7c38a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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:Screen
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54
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55 MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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56 Select the image to measure:DNA
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57 Measure the intensity only from areas enclosed by objects?:No
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58 Select the input objects:None
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59 Select the image to measure:DNA
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60 Measure the intensity only from areas enclosed by objects?:Yes
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61 Select the input objects:Nuclei