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annotate test-data/ExampleHuman.cppipe @ 2:b44b081bcf37 draft default tip

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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 09:39:27 +0000
parents 39006f6fd6bf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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1 CellProfiler Pipeline: http://www.cellprofiler.org
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2 Version:3
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3 DateRevision:300
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4 GitHash:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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5 ModuleCount:14
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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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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9 :
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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10 Filter images?:Images only
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11 Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.")
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12
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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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]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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14 Extract metadata?:No
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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<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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21 Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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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:\x5B\x5D
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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\'DNA\x3A DNA stained with DAPI\', \'PH3\x3A An antibody for phosphorylated histone H3 correlated with mitosis\', \'cellbody\x3A \'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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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:\x5B\x5D
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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:3
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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 contain "d0.tif")
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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 Maximum intensity:255.0
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48 Select the rule criteria:and (file does contain "d1.tif")
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49 Name to assign these images:PH3
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50 Name to assign these objects:Cell
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51 Select the image type:Grayscale image
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52 Set intensity range from:Image metadata
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53 Maximum intensity:255.0
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54 Select the rule criteria:and (file does contain "d2.tif")
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55 Name to assign these images:cellbody
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56 Name to assign these objects:Cell
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57 Select the image type:Grayscale image
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58 Set intensity range from:Image metadata
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59 Maximum intensity:255.0
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60
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61 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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62 Do you want to group your images?:No
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63 grouping metadata count:1
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64 Metadata category:None
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65
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66 IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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67 Select the input image:DNA
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68 Name the primary objects to be identified:Nuclei
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69 Typical diameter of objects, in pixel units (Min,Max):8,80
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70 Discard objects outside the diameter range?:Yes
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71 Discard objects touching the border of the image?:Yes
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72 Method to distinguish clumped objects:Intensity
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73 Method to draw dividing lines between clumped objects:Intensity
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74 Size of smoothing filter:10
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75 Suppress local maxima that are closer than this minimum allowed distance:7.0
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76 Speed up by using lower-resolution image to find local maxima?:Yes
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77 Fill holes in identified objects?:After declumping only
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78 Automatically calculate size of smoothing filter for declumping?:Yes
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79 Automatically calculate minimum allowed distance between local maxima?:Yes
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80 Handling of objects if excessive number of objects identified:Continue
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81 Maximum number of objects:500
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82 Use advanced settings?:No
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83 Threshold setting version:10
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84 Threshold strategy:Global
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85 Thresholding method:Minimum cross entropy
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86 Threshold smoothing scale:1.3488
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diff changeset
87 Threshold correction factor:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
88 Lower and upper bounds on threshold:0.0,1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
89 Manual threshold:0.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
90 Select the measurement to threshold with:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
91 Two-class or three-class thresholding?:Two classes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
92 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
93 Size of adaptive window:50
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
94 Lower outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
95 Upper outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
96 Averaging method:Mean
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
97 Variance method:Standard deviation
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
98 # of deviations:2.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
99 Thresholding method:Otsu
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
100
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
101 IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
102 Select the input image:PH3
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
103 Name the primary objects to be identified:PH3
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
104 Typical diameter of objects, in pixel units (Min,Max):8,80
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
105 Discard objects outside the diameter range?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
106 Discard objects touching the border of the image?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
107 Method to distinguish clumped objects:Intensity
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
108 Method to draw dividing lines between clumped objects:Intensity
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
109 Size of smoothing filter:10
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
110 Suppress local maxima that are closer than this minimum allowed distance:7.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
111 Speed up by using lower-resolution image to find local maxima?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
112 Fill holes in identified objects?:After declumping only
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
113 Automatically calculate size of smoothing filter for declumping?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
114 Automatically calculate minimum allowed distance between local maxima?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
115 Handling of objects if excessive number of objects identified:Continue
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
116 Maximum number of objects:500
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
117 Use advanced settings?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
118 Threshold setting version:10
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
119 Threshold strategy:Global
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
120 Thresholding method:Minimum cross entropy
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
121 Threshold smoothing scale:1.3488
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
122 Threshold correction factor:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
123 Lower and upper bounds on threshold:0.0,1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
124 Manual threshold:0.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
125 Select the measurement to threshold with:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
126 Two-class or three-class thresholding?:Two classes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
127 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
128 Size of adaptive window:50
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
129 Lower outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
130 Upper outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
131 Averaging method:Mean
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
132 Variance method:Standard deviation
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
133 # of deviations:2.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
134 Thresholding method:Otsu
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
135
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
136 RelateObjects:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
137 Parent objects:Nuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
138 Child objects:PH3
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
139 Calculate child-parent distances?:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
140 Calculate per-parent means for all child measurements?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
141 Calculate distances to other parents?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
142 Parent name:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
143
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
144 IdentifySecondaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
145 Select the input objects:Nuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
146 Name the objects to be identified:Cells
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
147 Select the method to identify the secondary objects:Propagation
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
148 Select the input image:cellbody
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
149 Number of pixels by which to expand the primary objects:10
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
150 Regularization factor:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
151 Discard secondary objects touching the border of the image?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
152 Discard the associated primary objects?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
153 Name the new primary objects:FilteredNuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
154 Fill holes in identified objects?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
155 Threshold setting version:10
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
156 Threshold strategy:Global
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
157 Thresholding method:Otsu
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
158 Threshold smoothing scale:0.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
159 Threshold correction factor:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
160 Lower and upper bounds on threshold:0.0,1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
161 Manual threshold:0.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
162 Select the measurement to threshold with:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
163 Two-class or three-class thresholding?:Three classes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
164 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
165 Size of adaptive window:50
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
166 Lower outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
167 Upper outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
168 Averaging method:Mean
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
169 Variance method:Standard deviation
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
170 # of deviations:2.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
171 Thresholding method:Otsu
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
172
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
173 IdentifyTertiaryObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
174 Select the larger identified objects:Cells
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
175 Select the smaller identified objects:Nuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
176 Name the tertiary objects to be identified:Cytoplasm
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
177 Shrink smaller object prior to subtraction?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
178
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
179 MeasureObjectIntensity:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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180 Hidden:2
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
181 Select an image to measure:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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182 Select an image to measure:PH3
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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183 Select objects to measure:Nuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
184 Select objects to measure:Cells
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
185 Select objects to measure:Cytoplasm
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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186
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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187 MeasureObjectSizeShape:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
188 Select objects to measure:Nuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
189 Select objects to measure:Cells
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
190 Select objects to measure:Cytoplasm
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
191 Calculate the Zernike features?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
192
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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193 OverlayOutlines:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
194 Display outlines on a blank image?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
195 Select image on which to display outlines:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
196 Name the output image:OrigOverlay
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
197 Outline display mode:Color
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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198 Select method to determine brightness of outlines:Max of image
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
199 How to outline:Thick
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
200 Select outline color:#0080FF
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
201 Select objects to display:Cells
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
202 Select outline color:blue
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
203 Select objects to display:Nuclei
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
204 Select outline color:yellow
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
205 Select objects to display:PH3
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
206
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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207 SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
208 Select the type of image to save:Image
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
209 Select the image to save:OrigOverlay
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
210 Select method for constructing file names:From image filename
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
211 Select image name for file prefix:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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212 Enter single file name:OrigBlue
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
213 Number of digits:4
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
214 Append a suffix to the image file name?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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215 Text to append to the image name:_Overlay
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
216 Saved file format:png
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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217 Output file location:Default Output Folder\x7C
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
218 Image bit depth:8-bit integer
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
219 Overwrite existing files without warning?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
220 When to save:Every cycle
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
221 Record the file and path information to the saved image?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
222 Create subfolders in the output folder?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
223 Base image folder:Elsewhere...\x7C
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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diff changeset
224
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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225 ExportToSpreadsheet:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
226 Select the column delimiter:Comma (",")
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
227 Add image metadata columns to your object data file?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
228 Select the measurements to export:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
229 Calculate the per-image mean values for object measurements?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
230 Calculate the per-image median values for object measurements?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
231 Calculate the per-image standard deviation values for object measurements?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
232 Output file location:Default Output Folder\x7C
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
233 Create a GenePattern GCT file?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
234 Select source of sample row name:Metadata
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
235 Select the image to use as the identifier:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
236 Select the metadata to use as the identifier:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
237 Export all measurement types?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
238 Press button to select measurements:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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239 Representation of Nan/Inf:NaN
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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parents:
diff changeset
240 Add a prefix to file names?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
241 Filename prefix:MyExpt_
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
242 Overwrite existing files without warning?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
243 Data to export:Do not use
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
244 Combine these object measurements with those of the previous object?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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245 File name:DATA.csv
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
246 Use the object name for the file name?:Yes