Mercurial > repos > bgruening > cp_cellprofiler
annotate starting_modules.py @ 3:a98608f3abc5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author | bgruening |
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date | Mon, 11 May 2020 07:50:04 -0400 |
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children | e917a2424690 |
rev | line source |
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3
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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1 import json |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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2 import sys |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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3 import os |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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4 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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5 FOURSPACES = " " |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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6 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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7 input_json_path = sys.argv[1] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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8 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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9 params = json.load(open(input_json_path, "r")) |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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10 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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11 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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12 def write_images(): |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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13 filter_images = params['images']['filter_images'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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14 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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15 _str = "\nImages:[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]\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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16 _str += FOURSPACES+":\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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17 _str += FOURSPACES + "Filter images?:%s\n" % filter_images |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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18 _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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19 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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20 return _str |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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21 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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22 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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23 def write_metadata(): |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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24 metadata_extraction = params['metadata']['con_metadata_extraction'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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25 extract = metadata_extraction['extract'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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26 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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27 if 'extraction_method' in metadata_extraction: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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28 method_count = len(metadata_extraction['extraction_method']) |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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29 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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30 method_count = 1 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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31 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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32 _str = "\nMetadata:[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]\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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33 _str += FOURSPACES + "Extract metadata?:%s\n" % extract |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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34 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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35 if extract == "No": |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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36 _str += FOURSPACES + "Metadata data type:Text\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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37 _str += FOURSPACES + "Metadata types:{}\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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38 _str += FOURSPACES + "Extraction method count:%d\n" % method_count |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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39 _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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40 _str += FOURSPACES + "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)\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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41 _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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42 _str += FOURSPACES + "Extract metadata from:All images\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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43 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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44 _str += FOURSPACES + "Metadata file location:\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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45 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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46 _str += FOURSPACES + "Use case insensitive matching?:No\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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47 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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48 _str += FOURSPACES + "Metadata data type:Text\n" #default Text,not possible to select in Galaxy |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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49 _str += FOURSPACES + "Metadata types:{}\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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50 _str += FOURSPACES + "Extraction method count:%d\n" % method_count |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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51 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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52 for methods in metadata_extraction["extraction_method"]: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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53 _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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54 _str += FOURSPACES + "Metadata source:%s\n" % methods["con_metadata_source"]["metadata_source"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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55 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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56 if "file_name_regex" in methods["con_metadata_source"]: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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57 file_regex = methods["con_metadata_source"]["file_name_regex"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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58 folder_regex = "(?P<folderField1>.*)" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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59 elif "folder_name_regex" in methods["con_metadata_source"]: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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60 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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61 folder_regex = methods["con_metadata_source"]["folder_name_regex"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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62 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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63 # default regex |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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64 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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65 folder_regex = "(?P<folderField1>.*)" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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66 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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67 _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % file_regex |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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68 _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % folder_regex |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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69 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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70 _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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71 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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72 if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule": |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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73 rule_str ="" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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74 for r in methods["con_metadata_extract_from"]["r_match"]: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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75 if r["con_match"]["rule_type"] == "extension": |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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76 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \ |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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77 r["con_match"]["match_type"]+")" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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78 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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79 rule_str +=" (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\ |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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changeset
|
80 r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] +"\")" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
81 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
82 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
83 _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str +"\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
84 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
85 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" #this line is required even if it's not used |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
86 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
87 _str += FOURSPACES + "Metadata file location:\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
88 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
89 _str += FOURSPACES + "Use case insensitive matching?:No\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
90 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
91 return _str |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
92 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
93 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
94 def write_nameandtypes(): |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
95 nameandtypes = params['nameandtypes'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
96 assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
97 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
98 if "con_select_image_type" in nameandtypes['con_assign_a_name_to']: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
99 con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
100 max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
101 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
102 max_intensity = 255.0 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
103 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
104 pixel_space = nameandtypes['pixel_space'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
105 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
106 rule_count = len(nameandtypes['con_assign_a_name_to']['r_match_rule']) if "r_match_rule" in nameandtypes['con_assign_a_name_to'] else 1 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
107 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
108 process_3d = nameandtypes['pixel_space']['process_3d'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
109 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
110 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
111 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
112 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
113 _str = "\nNamesAndTypes:[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]\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
114 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
115 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
116 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
117 if assign_a_name == "All images": |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
118 _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
119 _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
120 _str += FOURSPACES + "Match metadata:[]\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
121 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
122 _str += FOURSPACES + "Image set matching method:Order\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
123 _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
124 _str += FOURSPACES + "Assignments count:%s\n" % rule_count |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
125 _str += FOURSPACES + "Single images count:0\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
126 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
127 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
128 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
129 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
130 #the below lines are not relevant to "images matching rules", but needed in pipeline file |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
131 _str += FOURSPACES + "Select the image type:Grayscale image\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
132 _str += FOURSPACES + "Name to assign these images:DNA\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
133 _str += FOURSPACES + "Match metadata:[]\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
134 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
135 _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method'] |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
136 _str += FOURSPACES + "Set intensity range from:Image metadata\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
137 _str += FOURSPACES + "Assignments count:%d\n" % rule_count |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
138 _str += FOURSPACES + "Single images count:0\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
139 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
140 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
141 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
142 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
143 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
144 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
145 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
146 if assign_a_name == "Images matching rules": |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
147 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
148 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
149 rule_str = "" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
150 if len(rule["r_match"]) >0 : |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
151 for r in rule["r_match"]: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
152 if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory": |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
153 rule_str += " (" + r["con_match"]["rule_type"] + " "+r["con_match"]["operator"]+" "+\ |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
154 r["con_match"]["contain"]+" \"" + r["con_match"]["match_value"] +"\")" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
155 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
156 rule_str += " ("+ r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \ |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
157 r["con_match"]["match_type"] + ")" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
158 else: |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
159 rule_str = " (file does contain \"\")" #need to have a value even if it is not used |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
160 |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff
changeset
|
161 _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str +"\n" |
a98608f3abc5
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162 |
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163 img_or_obj = rule["con_select_image_type"]["select_image_type"] |
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164 |
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165 if img_or_obj == "Objects": |
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166 _str += FOURSPACES + "Name to assign these images:DNA\n" |
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167 _str += FOURSPACES + "Name to assign these objects:%s\n" % rule["con_select_image_type"]["name_to_assign"] |
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168 else: |
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169 _str += FOURSPACES + "Name to assign these images:%s\n" % rule["con_select_image_type"]["name_to_assign"] |
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170 _str += FOURSPACES + "Name to assign these objects:Cell\n" |
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171 |
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172 _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj |
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173 |
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174 |
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175 intensity_range="Image metadata" #default value |
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176 if img_or_obj == "Grayscale image" or img_or_obj == "Color image": |
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177 intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"] |
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178 |
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179 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range |
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180 |
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181 if intensity_range == "Manual": |
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182 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"] |
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183 else: |
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184 _str += FOURSPACES + "Maximum intensity:255.0\n" |
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185 |
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186 |
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187 return _str |
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188 |
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189 |
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190 def write_groups(): |
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191 groups = params['groups'] |
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192 |
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193 _str = "\nGroups:[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]\n" |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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194 |
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195 group_images = groups["con_groups"]["group_images"] |
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196 |
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197 _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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198 _str += FOURSPACES + "grouping metadata count:1\n" |
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199 |
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200 if group_images == "Yes": |
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201 _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"] |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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202 else: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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203 _str += FOURSPACES + "Metadata category:None\n" |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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204 |
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205 return _str |
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206 |
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207 |
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208 with open("output.cppipe", "w") as f: |
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209 headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n", |
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210 "Version:3\n", |
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211 "DateRevision:319\n", |
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212 "GitHash:\n", |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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213 "ModuleCount:4\n", |
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214 "HasImagePlaneDetails:False", |
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215 "\n"] |
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216 |
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217 f.writelines(headers) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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218 |
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219 img_str = write_images() |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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220 metadata_str = write_metadata() |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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221 nameandtypes_str = write_nameandtypes() |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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222 groups_str = write_groups() |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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223 |
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224 output_str = img_str + metadata_str + nameandtypes_str + groups_str |
a98608f3abc5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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225 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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226 f.write(output_str) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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227 f.close() |