Mercurial > repos > bgruening > cp_display_data_on_image

annotate test-data/export_to_spreadsheet.cppipe @ 3:4e12ef887a2a 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 07:55:32 -0400
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children 6a7da2e5f696
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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
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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: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]
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9 :
4e12ef887a2a "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
4e12ef887a2a "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]
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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14 Extract metadata?:Yes
4e12ef887a2a "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:{}
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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]+)
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:All images
4e12ef887a2a "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 "")
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24 Metadata file location:
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25 Match file and image metadata:[]
4e12ef887a2a "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
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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]
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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29 Assign a name to:Images matching rules
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30 Select the image type:Grayscale image
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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44 Name to assign these objects:Cell
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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 ExportToSpreadsheet:[module_num:5|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]
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56 Select the column delimiter:Tab
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57 Add image metadata columns to your object data file?:Yes
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58 Select the measurements to export:No
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59 Calculate the per-image mean values for object measurements?:Yes
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60 Calculate the per-image median values for object measurements?:Yes
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61 Calculate the per-image standard deviation values for object measurements?:Yes
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62 Output file location:Default Output Folder\x7C
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63 Create a GenePattern GCT file?:No
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64 Select source of sample row name:Metadata
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65 Select the image to use as the identifier:None
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66 Select the metadata to use as the identifier:None
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67 Export all measurement types?:Yes
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68 Press button to select measurements:
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69 Representation of Nan/Inf:NaN
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70 Add a prefix to file names?:No
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71 Filename prefix:MyPrefix_
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72 Overwrite existing files without warning?:Yes
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73 Data to export:Do not use
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74 Combine these object measurements with those of the previous object?:No
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75 File name:DATA.csv
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76 Use the object name for the file name?:Yes