Mercurial > repos > bgruening > cp_track_objects

annotate starting_modules.py @ 2:972d2c365739 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:31:44 +0000
parents 1fd453cd757b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
1 import json
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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2 import sys
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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4 FOURSPACES = " "
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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6 input_json_path = sys.argv[1]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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8 params = json.load(open(input_json_path, "r"))
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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11 def write_images():
2
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12 filter_images = params["images"]["filter_images"]
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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13
1
1fd453cd757b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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14 _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"
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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15 _str += FOURSPACES + ":\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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16 _str += FOURSPACES + "Filter images?:%s\n" % filter_images
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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17 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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18 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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19 + 'Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")\n'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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20 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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22 return _str
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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25 def write_metadata():
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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26 metadata_extraction = params["metadata"]["con_metadata_extraction"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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27 extract = metadata_extraction["extract"]
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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28
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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29 if "extraction_method" in metadata_extraction:
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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30 method_count = len(metadata_extraction["extraction_method"])
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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31 else:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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32 method_count = 1
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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33
1
1fd453cd757b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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34 _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"
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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35 _str += FOURSPACES + "Extract metadata?:%s\n" % extract
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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36
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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37 if extract == "No":
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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38 _str += FOURSPACES + "Metadata data type:Text\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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39 _str += FOURSPACES + "Metadata types:{}\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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40 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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41 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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42 FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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43 )
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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44 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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45 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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46 + "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"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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47 )
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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48 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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49 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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50 + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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51 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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52 _str += FOURSPACES + "Extract metadata from:All images\n"
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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53 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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54 FOURSPACES + 'Select the filtering criteria:and (file does contain "")\n'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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55 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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56 _str += FOURSPACES + "Metadata file location:\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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57 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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58 _str += FOURSPACES + "Use case insensitive matching?:No\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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59 else:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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60 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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61 FOURSPACES + "Metadata data type:Text\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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62 ) # default Text,not possible to select in Galaxy
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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63 _str += FOURSPACES + "Metadata types:{}\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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64 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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65
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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66 for methods in metadata_extraction["extraction_method"]:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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67 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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68 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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69 + "Metadata extraction method:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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70 % methods["metadata_extraction_method"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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71 )
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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72 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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73 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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74 + "Metadata source:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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75 % methods["con_metadata_source"]["metadata_source"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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76 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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77
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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78 if "file_name_regex" in methods["con_metadata_source"]:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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79 file_regex = methods["con_metadata_source"]["file_name_regex"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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80 folder_regex = "(?P<folderField1>.*)"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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81 elif "folder_name_regex" in methods["con_metadata_source"]:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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82 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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83 folder_regex = methods["con_metadata_source"]["folder_name_regex"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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84 else:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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85 # default regex
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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86 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff changeset
87 folder_regex = "(?P<folderField1>.*)"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
88
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
89 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
90 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
91 + "Regular expression to extract from file name:%s\n" % file_regex
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
92 )
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
93 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
94 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
95 + "Regular expression to extract from folder name:%s\n" % folder_regex
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
96 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
97
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
98 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
99 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
100 + "Extract metadata from:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
101 % methods["con_metadata_extract_from"]["extract_metadata_from"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
102 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
103
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
104 if (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
105 methods["con_metadata_extract_from"]["extract_metadata_from"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
106 == "Images matching a rule"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
107 ):
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
108 rule_str = ""
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
109 for r in methods["con_metadata_extract_from"]["r_match"]:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
110 if r["con_match"]["rule_type"] == "extension":
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
111 rule_str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
112 " ("
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
113 + r["con_match"]["rule_type"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
114 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
115 + r["con_match"]["operator"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
116 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
117 + r["con_match"]["match_type"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
118 + ")"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
119 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
120 else:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
121 rule_str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
122 " ("
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
123 + r["con_match"]["rule_type"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
124 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
125 + r["con_match"]["operator"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
126 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
127 + r["con_match"]["contain"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
128 + ' "'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
129 + r["con_match"]["match_value"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
130 + '")'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
131 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
132
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
133 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
134 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
135 + "Select the filtering criteria:"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
136 + methods["con_metadata_extract_from"]["match_all_any"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
137 + rule_str
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
138 + "\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
139 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
140 else:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
141 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
142 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
143 + 'Select the filtering criteria:and (file does contain "")\n'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
144 ) # this line is required even if it's not used
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
145
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
146 _str += FOURSPACES + "Metadata file location:\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
147 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
148 _str += FOURSPACES + "Use case insensitive matching?:No\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
149
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
150 return _str
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
151
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
152
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
153 def write_nameandtypes():
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
154 nameandtypes = params["nameandtypes"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
155 assign_a_name = nameandtypes["con_assign_a_name_to"]["assign_a_name_to"]
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
156
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
157 if "con_select_image_type" in nameandtypes["con_assign_a_name_to"]:
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
158 con_set_intensity = nameandtypes["con_assign_a_name_to"][
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
159 "con_select_image_type"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
160 ]["con_set_intensity"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
161 max_intensity = (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
162 con_set_intensity["maximum_intensity"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
163 if "maximum_intensity" in con_set_intensity
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
164 else 255.0
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
165 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
166 else:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
167 max_intensity = 255.0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
168
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
169 pixel_space = nameandtypes["pixel_space"]
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
170
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
171 rule_count = (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
172 len(nameandtypes["con_assign_a_name_to"]["r_match_rule"])
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
173 if "r_match_rule" in nameandtypes["con_assign_a_name_to"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
174 else 1
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
175 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
176
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
177 process_3d = nameandtypes["pixel_space"]["process_3d"]
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
178 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
179 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
180 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
181
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
182 _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"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
183
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
184 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
185
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
186 if assign_a_name == "All images":
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
187 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
188 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
189 + "Select the image type:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
190 % nameandtypes["con_assign_a_name_to"]["con_select_image_type"][
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
191 "select_image_type"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
192 ]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
193 )
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
194 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
195 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
196 + "Name to assign these images:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
197 % nameandtypes["con_assign_a_name_to"]["name_to_assign"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
198 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
199 _str += FOURSPACES + "Match metadata:[]\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
200
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
201 _str += FOURSPACES + "Image set matching method:Order\n"
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
202 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
203 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
204 + "Set intensity range from:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
205 % con_set_intensity["set_intensity_range_from"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
206 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
207 _str += FOURSPACES + "Assignments count:%s\n" % rule_count
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
208 _str += FOURSPACES + "Single images count:0\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
209 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
210 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
211
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
212 else:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
213 # the below lines are not relevant to "images matching rules", but needed in pipeline file
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
214 _str += FOURSPACES + "Select the image type:Grayscale image\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
215 _str += FOURSPACES + "Name to assign these images:DNA\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
216 _str += FOURSPACES + "Match metadata:[]\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
217
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
218 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
219 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
220 + "Image set matching method:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
221 % nameandtypes["con_assign_a_name_to"]["matching_method"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
222 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
223 _str += FOURSPACES + "Set intensity range from:Image metadata\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
224 _str += FOURSPACES + "Assignments count:%d\n" % rule_count
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
225 _str += FOURSPACES + "Single images count:0\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
226 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
227 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
228
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
229 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
230 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
231 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
232
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
233 if assign_a_name == "Images matching rules":
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
234 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
235
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
236 rule_str = ""
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
237 if len(rule["r_match"]) > 0:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
238 for r in rule["r_match"]:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
239 if (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
240 r["con_match"]["rule_type"] == "file"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
241 or r["con_match"]["rule_type"] == "directory"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
242 ):
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
243 rule_str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
244 " ("
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
245 + r["con_match"]["rule_type"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
246 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
247 + r["con_match"]["operator"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
248 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
249 + r["con_match"]["contain"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
250 + ' "'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
251 + r["con_match"]["match_value"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
252 + '")'
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
253 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
254 else:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
255 rule_str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
256 " ("
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
257 + r["con_match"]["rule_type"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
258 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
259 + r["con_match"]["operator"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
260 + " "
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
261 + r["con_match"]["match_type"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
262 + ")"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
263 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
264 else:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
265 rule_str = ' (file does contain "")' # need to have a value even if it is not used
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
266
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
267 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
268 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
269 + "Select the rule criteria:"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
270 + rule["match_all_any"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
271 + rule_str
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
272 + "\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
273 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
274
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
275 img_or_obj = rule["con_select_image_type"]["select_image_type"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
276
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
277 if img_or_obj == "Objects":
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
278 _str += FOURSPACES + "Name to assign these images:DNA\n"
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
279 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
280 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
281 + "Name to assign these objects:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
282 % rule["con_select_image_type"]["name_to_assign"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
283 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
284 else:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
285 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
286 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
287 + "Name to assign these images:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
288 % rule["con_select_image_type"]["name_to_assign"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
289 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
290 _str += FOURSPACES + "Name to assign these objects:Cell\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
291
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
292 _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
293
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
294 intensity_range = "Image metadata" # default value
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
295 if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
296 intensity_range = rule["con_select_image_type"]["con_set_intensity"][
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
297 "set_intensity_range_from"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
298 ]
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
299
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
300 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
301
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
302 if intensity_range == "Manual":
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
303 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
304 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
305 + "Maximum intensity:%s\n"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
306 % rule["con_select_image_type"]["con_set_intensity"][
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
307 "maximum_intensity"
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
308 ]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
309 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
310 else:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
311 _str += FOURSPACES + "Maximum intensity:255.0\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
312
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
313 return _str
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
314
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
315
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
316 def write_groups():
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
317 groups = params["groups"]
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
318
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
319 _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"
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
320
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
321 group_images = groups["con_groups"]["group_images"]
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
322
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
323 _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
324 _str += FOURSPACES + "grouping metadata count:1\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
325
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
326 if group_images == "Yes":
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
327 _str += (
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
328 FOURSPACES
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
329 + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
330 )
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
331 else:
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
332 _str += FOURSPACES + "Metadata category:None\n"
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
333
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
334 return _str
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
335
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
336
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
337 with open("output.cppipe", "w") as f:
2
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
338 headers = [
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
339 "CellProfiler Pipeline: http://www.cellprofiler.org\n",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
340 "Version:3\n",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
341 "DateRevision:319\n",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
342 "GitHash:\n",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
343 "ModuleCount:4\n",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
344 "HasImagePlaneDetails:False",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
345 "\n",
972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 1
diff changeset
346 ]
0
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
347
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
348 f.writelines(headers)
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
349
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
350 img_str = write_images()
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
351 metadata_str = write_metadata()
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
352 nameandtypes_str = write_nameandtypes()
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
353 groups_str = write_groups()
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
354
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
355 output_str = img_str + metadata_str + nameandtypes_str + groups_str
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
356
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
357 f.write(output_str)
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
358 f.close()