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annotate common.xml @ 0:9c8ee01c0b22 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 16:23:56 -0400
parents
children 0b7db679fff8
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9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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1 <tool id="cp_common" name="cellProfiler common start modules" version="@CP_VERSION@">
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2 <description>load images and metadata into cellProfiler</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="image_type_condition">
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6 <conditional name="con_set_intensity">
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7 <param name="set_intensity_range_from" type="select" label="Set intensity range from">
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8 <option value="Image metadata">Image metadata</option>
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9 <option value="Image bit-depth">Image bit-depth</option>
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10 <option value="Manual">Manual</option>
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11 </param>
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12 <when value="Manual">
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13 <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity"/>
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14 </when>
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15 <when value="Image metadata" />
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16 <when value="Image bit-depth" />
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17 </conditional>
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18 </xml>
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19 <xml name="name_type_rule_matching_file">
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20 <param name="operator" type="select">
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21 <option value="does">Does</option>
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22 <option value="doesnot">Does not</option>
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23 </param>
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24 <param name="contain" type="select">
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25 <option value="contain">Contain</option>
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26 <option value="Contain regular expression">Contain regular expression</option>
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27 <option value="startwith">Start with</option>
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28 <option value="endwith">End with</option>
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29 <option value="Exactly match">Exactly match</option>
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30 </param>
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31 <param name="match_value" type="text"/>
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32 </xml>
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33 <xml name="image_matching_rules">
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34 <repeat name="r_match_rule" title="Rules">
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35 <param name="match_all_any" type="select" display="radio" label="Match the following rules">
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36 <option value="and">All</option>
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37 <option value="or">Any</option>
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38 </param>
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39 <conditional name="con_match">
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40 <param name="rule_type" type="select" label="Select rule criteria">
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41 <option value="file">File</option>
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42 <option value="directory">Directory</option>
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43 <option value="extension">Extension</option>
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44 <option value="image">Image</option>
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45 <option value="metadata">Metadata</option>
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46 </param>
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47 <when value="file">
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48 <expand macro="name_type_rule_matching_file"/>
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49 </when>
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50 <when value="directory">
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51 <expand macro="name_type_rule_matching_file"/>
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52 </when>
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53 <when value="extension" />
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54 <when value="image"/>
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55 <when value="metadata"/>
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56 </conditional>
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57 <param name="name_to_assign" label="Name to assign these images" type="text" />
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58 <conditional name="con_select_image_type">
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59 <param name="select_image_type" type="select" label="Select the image type">
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60 <option value="Grayscale image">Grayscale image</option>
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61 <option value="Color image">Color image</option>
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62 <option value="Binary mask">Binary mask</option>
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63 </param>
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64 <when value ="Grayscale image">
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65 <expand macro="image_type_condition" />
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66 </when>
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67 <when value="Color image">
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68 <expand macro="image_type_condition" />
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69 </when>
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70 <when value="Binary mask">
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71 </when>
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72 </conditional>
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73 </repeat>
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74 </xml>
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75 </macros>
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76 <expand macro="py_requirements"/>
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77
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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78 <command detect_errors="aggressive"><![CDATA[
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79 python '$script_file' '$inputs'
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80 ]]></command>
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81
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82 <configfiles>
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83 <inputs name="inputs"/>
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84 <configfile name="script_file">
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85 import json
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86 import sys
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87 import os
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88
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89 FOURSPACES = @SPACES@
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90
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91 input_json_path = sys.argv[1]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
93 params = json.load(open(input_json_path, "r"))
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
95
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96 def write_images():
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97 filter_images = params['images']['filter_images']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
99 _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"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
100 _str += FOURSPACES+":\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
101 _str += FOURSPACES + "Filter images?:%s\n" % filter_images
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
102 _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104 return _str
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
107 def write_metadata():
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
108 metadata_extraction = params['metadata']['con_metadata_extraction']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
109 extract = metadata_extraction['extract']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
110
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 if 'extraction_method' in metadata_extraction:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
112 method_count = len(metadata_extraction['extraction_method'])
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
113 else:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
114 method_count = 1
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116 _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"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117 _str += FOURSPACES + "Extract metadata?:%s\n" % extract
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119 if extract == "No":
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
120 _str += FOURSPACES + "Metadata data type:Text\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 _str += FOURSPACES + "Metadata types:{}\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
123 _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
124 _str += FOURSPACES + "Regular expression to extract from file name:^(?P&lt;Plate>.*)_(?P&lt;Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P&lt;Site>\x5B0-9\x5D)_w(?P&lt;ChannelNumber>\x5B0-9\x5D)\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
125 _str += FOURSPACES + "Regular expression to extract from folder name:(?P&lt;Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
126 _str += FOURSPACES + "Extract metadata from:All images\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
127 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128 _str += FOURSPACES + "Metadata file location:\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
129 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130 _str += FOURSPACES + "Use case insensitive matching?:No\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
131 else:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
132 _str += FOURSPACES + "Metadata data type:%s\n" % metadata_extraction['metadata_type']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
133 _str += FOURSPACES + "Metadata types:{}\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
134 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
135
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
136 for methods in metadata_extraction["extraction_method"]:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
137 _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
138 _str += FOURSPACES + "Metadata source:%s\n" % methods["metadata_source"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
139 _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % methods["file_name_regex"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
140 _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % methods["folder_name_regex"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
141 _str += FOURSPACES + "Extract metadata from:%s\n" % methods["extract_metadata_from"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
142 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
143 _str += FOURSPACES + "Metadata file location:\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
144 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
145 _str += FOURSPACES + "Use case insensitive matching?:No\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
146
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
147 return _str
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
148
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
149
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
150 def write_nameandtypes():
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
151 nameandtypes = params['nameandtypes']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
152 assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
153
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
154 if "con_select_image_type" in nameandtypes['con_assign_a_name_to']:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
155 con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
156 max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
157 else:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
158 max_intensity = 255.0
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
159
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
160 pixel_space = nameandtypes['pixel_space']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
161
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
162 rule_count = len(nameandtypes['r_match_rule']) if "r_match_rule" in nameandtypes else 1
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
163
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
164 process_3d = nameandtypes['pixel_space']['process_3d']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
165 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
166 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
167 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
168
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
169 _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"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
170
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
171 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
172
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
173 if assign_a_name == "All images":
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
174 _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
175 _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
176 _str += FOURSPACES + "Match metadata:[]\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
177
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
178 _str += FOURSPACES + "Image set matching method:Order\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
179 _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
180 _str += FOURSPACES + "Assignments count:%s\n" % rule_count
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
181 _str += FOURSPACES + "Single images count:0\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
182 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
183 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
184
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
185 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" + x_spacing
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
186 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" + y_spacing
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
187 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" + z_spacing
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
188 else:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
189 _str += FOURSPACES + "Select the image type:Grayscale image\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
190 _str += FOURSPACES + "Name to assign these images:DNA\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
191 _str += FOURSPACES + "Match metadata:[]\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
192
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
193 _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
194 _str += FOURSPACES + "Set intensity range from:Image metadata\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
195 _str += FOURSPACES + "Assignments count:%d\n" % rule_count
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
196 _str += FOURSPACES + "Single images count:0\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
197 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
198 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
199
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
200 _str += FOURSPACES + "Relative pixel spacing in X:1.0\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
201 _str += FOURSPACES + "Relative pixel spacing in Y:1.0\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
202 _str += FOURSPACES + "Relative pixel spacing in Z:1.0\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
203
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
204 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
205 _str += FOURSPACES + "Select the rule criteria:%s%s%s%s%s%s%s%s%s%s\n" % (rule["match_all_any"], " (",rule["con_match"]["rule_type"], " ",rule["con_match"]["operator"]," ",rule["con_match"]["contain"]," \"",rule["con_match"]["match_value"],"\")")
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
206 _str += FOURSPACES + "Name to assign these images:%s\n" % rule["name_to_assign"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
207 _str += FOURSPACES + "Name to assign these objects:Cell\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
208 _str += FOURSPACES + "Select the image type:%s\n" % rule["con_select_image_type"]["select_image_type"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
209
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
210 intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
211
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
212 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
213 _str += FOURSPACES + "Select the image type:%s\n" % rule["con_select_image_type"]["select_image_type"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
214
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
215 if intensity_range == "Manual":
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
216 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
217 else:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
218 _str += FOURSPACES + "Maximum intensity:255.0\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
219
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
220 if process_3d == "Yes":
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
221 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" + x_spacing
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
222 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" + y_spacing
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
223 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" + z_spacing
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
224
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
225 return _str
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
226
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
227
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
228 def write_groups():
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
229 groups = params['groups']
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
230
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
231 _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"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
232
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
233 _str += FOURSPACES + "Do you want to group your images?:%s\n" % groups["con_groups"]["group_images"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
234 _str += FOURSPACES + "grouping metadata count:1\n"
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
235 _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
236
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
237 return _str
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
238
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
239
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
240 with open("output", "w") as f:
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
241 headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n",
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
242 "Version:3\n",
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
243 "DateRevision:319\n",
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
244 "GitHash:\n",
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
245 "ModuleCount:4\n",
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
246 "HasImagePlaneDetails:False",
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
247 "\n"]
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
248
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
249 f.writelines(headers)
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
250
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
251 img_str = write_images()
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
252 metadata_str = write_metadata()
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
253 nameandtypes_str = write_nameandtypes()
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
254 groups_str = write_groups()
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
255
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
256 output_str = img_str + metadata_str + nameandtypes_str + groups_str
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
257
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258 f.write(output_str)
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259 f.close()
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260
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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261 </configfile>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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262 </configfiles>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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263 <inputs>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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264 <!-- Images module-->
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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265 <section name="images" title="Images" expanded="false">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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266 <param name="filter_images" type="select" label="Filer images?">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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267 <option value="Images only">Images only</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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268 <option value="No filtering">No filtering</option>
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269 </param>
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270 </section>
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271 <!-- Metadata module-->
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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272 <section name="metadata" title="Metadata" expanded="false">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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273 <conditional name="con_metadata_extraction">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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274 <param name="extract" type="select" display="radio" label="Extract metadata?">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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275 <option value="No">No</option>
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276 <option value="Yes">Yes</option>
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277 </param>
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278 <when value="Yes">
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279 <repeat name="extraction_method" title="metadata">
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280 <param name="metadata_extraction_method" type="select" label="Metadata extraction method">
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281 <option value="Extract from file/folder names">Extract from file/folder names</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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282 <option value="Import from file">Import from file</option>
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283 <option value="Extract from image file headers">Extract from image file headers</option>
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284 </param>
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285 <param name="metadata_source" type="select" label="Metadata source">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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286 <option value="File name">File name</option>
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287 <option value="Folder name">Folder name</option>
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288 </param>
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289 <param name="file_name_regex" type="select" label="Select file name pattern to extract from file name" help="Image file names must comply with one of the patterns.For example, AS_09125_050116030001_D03f00d0.tif matches the pattern field1_filed2_field3_field4. If none of the patterns are suitable, please use other Galaxy tools to rename your files first. ">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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290 <sanitizer sanitize="false"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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291 <option value="(?P&lt;field1>.*)">field1</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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292 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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293 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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294 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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295 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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296 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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297 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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298 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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299 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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300 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
301 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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302 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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303 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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304 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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305 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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306 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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307 </param>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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308 <param name="folder_name_regex" type="text" value="(?P&lt;Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$" label="Regular expression to extract from folder name">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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309 <sanitizer sanitize="false"/>
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310 </param>
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311 <param name="extract_metadata_from" type="select" label="Extract metadata from">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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312 <option value="All images">All images</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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313 <option value="Images matching a rule">Images matching a rule</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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314 </param>
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315 </repeat>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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316 <param name="metadata_type" type="select" label="Metadata data type">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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317 <option value="Text">Text</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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318 </param>
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319 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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320 <when value="No">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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321 </when>
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322 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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323 </section>
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324 <!-- NamesAndTypes-->
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325 <section name="nameandtypes" title="NamesAndTypes" expanded="false">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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326 <conditional name="pixel_space">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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327 <param name="process_3d" type="select" display="radio" label="Process 3D">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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328 <option value="No">No</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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329 <option value="Yes">Yes</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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330 </param>
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331 <when value="Yes">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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332 <param name="x_spacing" type="float" value="1.0" label="Relative pixel spacing in X"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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333 <param name="y_spacing" type="float" value="1.0" label="Relative pixel spacing in Y"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
334 <param name="z_spacing" type="float" value="1.0" label="Relative pixel spacing in Z"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
335 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
336 <when value="No">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
337 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
338 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
339 <conditional name="con_assign_a_name_to">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
340 <param name="assign_a_name_to" type="select" label="Assign a name to">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
341 <option value="All images">All images</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
342 <option value="Images matching rules">Images matching rules</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
343 </param>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
344 <when value="All images">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
345 <param name="name_to_assign" type="text" value="DNA" label="Name to assign these images"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
346 <conditional name="con_select_image_type">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
347 <param name="select_image_type" type="select" label="Select the image type">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
348 <option value="Grayscale image">Grayscale image</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
349 <option value="Color image">Color image</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
350 <option value="Binary mask">Binary mask</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
351 </param>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
352 <when value ="Grayscale image">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
353 <expand macro="image_type_condition" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
354 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
355 <when value="Color image">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
356 <expand macro="image_type_condition" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
357 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
358 <when value="Binary mask">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
359 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
360 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
361 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
362 <when value="Images matching rules">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
363 <expand macro="image_matching_rules"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
364 <param name="matching_method" type="select" label="Image set matching method">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
365 <option value="Order">Order</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
366 <option value="Metadata">Metadata</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
367 </param>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
368 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
369 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
370 </section>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
371 <!-- Groups -->
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
372 <section name="groups" title="Groups" expanded="false">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
373 <conditional name="con_groups">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
374 <param name="group_images" type="select" value="No" label="Do you want to group your images?" display="radio">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
375 <option value="Yes">Yes</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
376 <option value="No">No</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
377 </param>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
378 <when value="Yes">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
379 <param name="group_category" type="select" label="Metadata category">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
380 <option value="FileLocation">FileLocation</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
381 <option value="Frame">Frame</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
382 <option value="ImageId">ImageId</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
383 <option value="Screen">Screen</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
384 <option value="Series">Series</option>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
385 </param>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
386 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
387 <when value="No">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
388 </when>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
389 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
390 </section>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
391 </inputs>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
392 <outputs>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
393 <expand macro="output_pipeline_macro" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
394 </outputs>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
395 <tests>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
396 <test>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
397 <param name="filter_images" value="Images only"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
398 <conditional name="con_metadata_extraction">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
399 <param name="extract" value="Yes"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
400 <repeat name="extraction_method">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
401 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
402 <param name="metadata_source" value="File name" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
403 <param name="file_name_regex" value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
404 <param name="extract_metadata_from" value="All images" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
405 </repeat>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
406 <param name="metadata_type" value="Text" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
407 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
408 <conditional name="pixel_space">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
409 <param name="process_3d" value="No"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
410 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
411 <conditional name="con_assign_a_name_to">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
412 <param name="assign_a_name_to" value="Images matching rules"/>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
413 <repeat name="r_match_rule">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
414 <param name="match_all_any" value="and" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
415 <conditional name="con_match">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
416 <param name="rule_type" value="file" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
417 <param name="operator" value="does" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
418 <param name="contain" value="startwith" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
419 <param name="match_value" value="im" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
420 </conditional>
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
421 <param name="name_to_assign" value="DNA" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
422 <conditional name="con_select_image_type">
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
423 <param name="select_image_type" value="Grayscale image" />
9c8ee01c0b22 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
424 <conditional name="con_set_intensity">
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425 <param name="set_intensity_range_from" value="Image metadata" />
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426 </conditional>
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427 </conditional>
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428 </repeat>
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429 <param name="matching_method" value="Order" />
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430 </conditional>
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431 <conditional name="con_groups">
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432 <param name="group_images" value="Yes" />
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433 <param name="group_category" value="Screen" />
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434 </conditional>
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435 <expand macro="test_out_file" />
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436 </test>
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437 </tests>
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438
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439 <help>
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440 This tool builds a cellProfiler pipeline file with headers and 4 compulsory modules, 'Images', 'Metadata', 'NamesAndTypes' and 'Groups'.
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441
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442 No input parameters are needed for this tool. The rest CP modules will build based on the output of this file.
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443
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444
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445 Images: use the Images module to compile a list of files that you want to analyze.
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446
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447 Metadata: optionally allows you to extract information describing your images (i.e., metadata) which will be stored along with your measurements.
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448
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449 NamesAndTypes: allows you to assign a meaningful name to each image by which other modules will refer to it.
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450
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451 Groups: 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.
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452
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453 </help>
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454 <expand macro="citations" />
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455 </tool>