Mercurial > repos > bgruening > cp_save_images

annotate save_images.xml @ 5:33f4fa1413fb draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:09:57 +0000
parents a45d360ae9d9
children 27edbb90ab2b
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5
33f4fa1413fb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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1 <tool id="cp_save_images" name="SaveImages" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
3
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2 <description>or movie files</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
5
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6 <token name="@VERSION_SUFFIX@">1</token>
0
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7 <xml name="file_format">
3
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8 <param name="file_format" label="Saved the format to save the image(s)" type="select">
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9 <help>
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10 <![CDATA[
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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11 - Only tiff supports saving as 16-bit or 32-bit. tiff is a "lossless" file format.
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12 <br> - png is also a "lossless" file format and it tends to produce smaller files without losing any image data.
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13 <br> - jpeg is also small but is a "lossy" file format and should not be used for any images that will undergo further quantitative analysis.
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14 <br> - Select npy to save an illumination correction image generated by CorrectIlluminationCalculate.
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15 ]]>
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16 </help>
0
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17 <option value="jpeg">jpeg</option>
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18 <option value="npy">npy</option>
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19 <option value="png">png</option>
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20 <option value="tiff">tiff</option>
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21 </param>
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22 </xml>
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23 <xml name="bit_depth">
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24 <param name="bit_depth" label="Image bit depth" type="select">
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25 <help>
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26 <![CDATA[
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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27 Select the bit-depth at which you want to save the images.
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28 <br> - 32-bit floating point saves the image as floating-point decimals with 32-bit precision. When the input data is integer or binary type, pixel values are scaled within the range (0, 1). Floating point data is not rescaled.
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29 <br> - 16-bit integer and 32-bit floating point images are supported only for TIFF formats.
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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30 ]]>
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31 </help>
0
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32 <option value="8-bit integer">8-bit integer</option>
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33 <option value="16-bit integer">16-bit integer</option>
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34 <option value="32-bit floating point">32-bit floating point</option>
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35 </param>
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36 </xml>
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37 </macros>
3
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38
0
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39 <expand macro="py_requirements"/>
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40 <expand macro="cmd_modules" />
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41
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42 <configfiles>
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43 <inputs name="inputs" />
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44 <configfile name="script_file">
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45 import json
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46 import sys
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47 import os
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48
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49 FOURSPACES=@SPACES@
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50
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51 input_json_path = sys.argv[1]
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52 input_pipeline= sys.argv[2]
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53
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54 params = json.load(open(input_json_path, "r"))
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55
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56 def writesi():
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57 _str = "\nSaveImages:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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58
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59 _str += FOURSPACES + "Select the type of image to save:%s\n" % params['con_type_of_image']['type_of_image']
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61 _str += FOURSPACES + "Select the image to save:%s\n" % params['image_to_save']
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62
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63 method_for_constructing = params['con_method_for_constructing']['method_for_constructing']
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64 _str += FOURSPACES + "Select method for constructing file names:%s\n" % method_for_constructing
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65
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66 if method_for_constructing == "From image filename":
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67 img_name_file_prefix = params['con_method_for_constructing']['name_for_file_prefix']
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68 append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
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69
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70 if append_suffix == "Yes":
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71 text_append = params['con_method_for_constructing']['con_append_suffix']['text_to_append']
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72 else:
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73 text_append = ""
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74 else:
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75 img_name_file_prefix = "None"
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76 append_suffix = "No"
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77 text_append = ""
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78
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79 _str += FOURSPACES + "Select image name for file prefix:%s\n" % img_name_file_prefix
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80
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81 if method_for_constructing == "Sequential numbers":
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82 file_prefix = params['con_method_for_constructing']['file_prefix']
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83 no_of_digits = params['con_method_for_constructing']['no_of_digits']
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84
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85 _str += FOURSPACES + "Enter file prefix:%s\n" % file_prefix
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86 elif method_for_constructing == "Single name":
3
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87 _str += FOURSPACES + "Enter single file name:%s\n" % params['con_method_for_constructing']['single_file_name']
0
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88
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
89 no_of_digits = 4
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
90 else:
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91 _str += FOURSPACES + "Enter single file name:OrigBlue\n"
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92 no_of_digits = 4
5
33f4fa1413fb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
bgruening
parents: 3
diff changeset
93 append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
95 _str += FOURSPACES + "Number of digits:%d\n" % no_of_digits
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96 _str += FOURSPACES + "Append a suffix to the image file name?:%s\n" % append_suffix
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97 _str += FOURSPACES + "Text to append to the image name:%s\n" % text_append
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
99 save_format = params['con_type_of_image']['con_save_file_format']['file_format']
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
100
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
101 _str += FOURSPACES + "Saved file format:%s\n" % save_format
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
102
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103 if save_format == "tiff":
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104 bit_depth = params['con_type_of_image']['con_save_file_format']['bit_depth']
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105 else:
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106 bit_depth = "8-bit integer"
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
107
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
108 _str += FOURSPACES + "Output file location:Default Output Folder\\x7Coutput\n"
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
109 _str += FOURSPACES + "Image bit depth:%s\n" % bit_depth
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
110 _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params['overwrite_without_warning']
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 _str += FOURSPACES + "When to save:%s\n" % params['when_to_save']
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
112 _str += FOURSPACES + "Record the file and path information to the saved image?:%s\n" % params['record_info']
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
113 _str += FOURSPACES + "Create subfolders in the output folder?:No\n"
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
114 _str += FOURSPACES + "Base image folder:Elsewhere...\n"
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116 return _str
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118 with open(input_pipeline) as fin:
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119 lines = fin.readlines()
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
120
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 k, v = lines[4].strip().split(':')
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
123 module_count = int(v)
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
124 new_count = module_count + 1
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
125 lines[4] = k + ":%d\n" % new_count
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
126
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
127 with open("output.cppipe", "w") as f:
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128 f.writelines(lines)
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
129 f.write(writesi())
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
131 f.close()
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
132 </configfile>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
133 </configfiles>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
134
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
135 <inputs>
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
136 <expand macro="input_pipeline_param" />
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
137 <conditional name="con_type_of_image">
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
138 <param name="type_of_image" type="select" label="Select the type of image to save">
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
139 <help>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
140 <![CDATA[
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
141 The following types of images can be saved as a file on the hard drive:
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
142 <br> - Image: Any of the images produced upstream of SaveImages can be selected for saving. Outlines of objects created by other modules such as Identify modules, Watershed, and various object processing modules can also be saved with this option, but you must use the OverlayOutlines module to create them prior to saving images. Likewise, if you wish to save the objects themselves, you must use the ConvertObjectsToImage module to create a savable image.
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
143 <br> - Mask: Relevant only if a module that produces masks has been used such as Crop, MaskImage, or MaskObjects. These modules create a mask of the pixels of interest in the image. Saving the mask will produce a binary image in which the pixels of interest are set to 1; all other pixels are set to 0.
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
144 <br> - Cropping: Relevant only if the Crop module is used. The Crop module also creates a cropping image which is typically the same size as the original image. However, since Crop permits removal of the rows and columns that are left blank, the cropping can be of a different size than the mask.
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
145 <br> - Movie: A sequence of images can be saved as a TIFF stack.
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
146 ]]>
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
147 </help>
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
148 <option value="Image">Image</option>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
149 <option value="Mask">Mask</option>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
150 <option value="Cropping">Cropping</option>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
151 <option value="Movie">Movie</option>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
152 </param>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
153 <when value="Image">
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
154 <conditional name="con_save_file_format">
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
155 <expand macro="file_format" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
156 <when value="tiff">
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
157 <expand macro="bit_depth" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
158 </when>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
159 <when value="jpeg" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
160 <when value="npy" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
161 <when value="png" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
162 </conditional>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
163 </when>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
164 <when value="Mask">
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
165 <expand macro="file_format" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
166 </when>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
167 <when value="Cropping">
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
168 <expand macro="file_format" />
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
169 </when>
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
170 <when value="Movie">
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
171 <expand macro="bit_depth" />
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
172 </when>
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
173 </conditional>
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
174 <param name="image_to_save" label="Enter the name of the image to save" type="text" />
0
6e0f244acd32 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
175 <conditional name="con_method_for_constructing">
3
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
176 <param name="method_for_constructing" label="Select method for constructing file names" type="select">
a45d360ae9d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
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177 <help>
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178 <![CDATA[
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179 Several choices are available for constructing the image file name:
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180 <br> - From image filename: The filename will be constructed based on the original filename of an input image specified in NamesAndTypes.
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181 You will have the opportunity to prefix or append additional text.
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182 If you have metadata associated with your images, you can append text to the image filename using a metadata tag.
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183 This is especially useful if you want your output given a unique label according to the metadata corresponding to an image group.
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184 The name of the metadata to substitute can be provided for each image for each cycle using the Metadata module.
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185 <br> - Sequential numbers: Same as above, but in addition, each filename will have a number appended to the end that corresponds to the image cycle number (starting at 1).
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186 <br> - Single name: A single name will be given to the file. Since the filename is fixed, this file will be overwritten with each cycle. In this case, you would probably want to save the image on the last cycle (see the Select how often to save setting). The exception to this is to use a metadata tag to provide a unique label, as mentioned in the From image filename option.
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187 ]]>
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188 </help>
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189 <option value="From image filename">From image filename</option>
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190 <option value="Sequential numbers">Sequential numbers</option>
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191 <option value="Single name">Single name</option>
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192 </param>
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193 <when value="From image filename">
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194 <param name="name_for_file_prefix" label="Enter the image name (from NamesAndTypes) to be used as file prefix" type="text">
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195 <expand macro="text_validator" />
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196 </param>
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197 <conditional name="con_append_suffix">
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198 <param name="append_suffix" type="select" display="radio" label="Append a suffix to the image file name?">
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199 <option value="Yes">Yes</option>
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200 <option value="No" selected="True">No</option>
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201 </param>
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202 <when value="Yes">
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203 <param name="text_to_append" label="Text to append to the image name" type="text">
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204 <expand macro="text_validator" />
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205 </param>
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206 </when>
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207 <when value="No" />
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208 </conditional>
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209 </when>
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210 <when value="Sequential numbers">
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211 <param name="file_prefix" label="Enter file prefix" value="OrigBlue" type="text"/>
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212 <param name="no_of_digits" label="Number of digits" type="integer" value="4" min="0" help="Specify the number of digits to be used for the sequential numbering. Zeros will be used to left-pad the digits. If the number specified here is less than that needed to contain the number of image sets, the latter will override the value entered."/>
0
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213 </when>
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214 <when value="Single name">
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215 <param name="single_file_name" label="Enter single file name" value="OrigBlue" type="text">
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216 <expand macro="text_validator" />
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217 </param>
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218 </when>
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219 </conditional>
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220 <param name="overwrite_without_warning" label="Overwrite existing files without warning?" type="select" display="radio">
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221 <option value="Yes">Yes</option>
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222 <option value="No" selected="True">No</option>
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223 </param>
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224 <param name="when_to_save" label="When to save" type="select">
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225 <help>
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226 <![CDATA[
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227 Specify at what point during pipeline execution to save file(s).
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228 <br> - Every cycle: Useful for when the image of interest is created every cycle and is not dependent on results from a prior cycle.
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229 <br> - First cycle: Useful for when you are saving an aggregate image created on the first cycle, e.g., CorrectIlluminationCalculate with the 'All setting' used on images obtained directly from NamesAndTypes.
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230 <br> - Last cycle: Useful for when you are saving an aggregate image completed on the last cycle, e.g., CorrectIlluminationCalculate with the 'All setting' used on intermediate images generated during each cycle.
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231 ]]>
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232 </help>
0
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233 <option value="Every cycle">Every cycle</option>
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234 <option value="First cycle">First cycle</option>
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235 <option value="Last cycle">Last cycle</option>
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236 </param>
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237 <param name="record_info" label="Record the file and path information to the saved image?" type="select" display="radio">
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238 <option value="Yes">Yes</option>
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239 <option value="No" selected="True">No</option>
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240 </param>
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241
0
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242 </inputs>
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243
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244 <outputs>
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245 <expand macro="output_pipeline_param" />
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246 </outputs>
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247
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248 <tests>
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249 <test>
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250 <expand macro="test_input_pipeline_param" />
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251
0
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252 <conditional name="con_type_of_image">
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253 <param name="type_of_image" value="Image" />
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254 <conditional name="con_save_file_format">
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255 <param name="file_format" value="tiff" />
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256 <param name="bit_depth" value="8-bit integer" />
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257 </conditional>
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258 </conditional>
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259 <param name="image_to_save" value="ImageDisplay" />
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260 <conditional name="con_method_for_constructing">
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261 <param name="method_for_constructing" value="From image filename" />
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262 <param name="name_for_file_prefix" value="DNA" />
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263 <conditional name="con_append_suffix">
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264 <param name="append_suffix" value="Yes" />
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265 <param name="text_to_append" value="_nucleiNumbers" />
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266 </conditional>
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267 </conditional>
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268 <param name="overwrite_without_warning" value="Yes" />
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269 <param name="when_to_save" value="Every cycle" />
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270 <param name="record_info" value="No" />
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271 <param name="subfolder_in_output" value="No" />
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272
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273 <expand macro="test_out_file" file="save_images.cppipe" />
0
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274
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275 </test>
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276 </tests>
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277
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278 <help>
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279 <![CDATA[
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280
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281 .. class:: infomark
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282
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283 **What it does**
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284
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285 SaveImages saves image or movie files.
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286 Because CellProfiler usually performs many image analysis steps on many groups of images, it does not save any of the resulting images to the hard drive unless you specifically choose to do so with the SaveImages module.
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287 You can save any of the processed images created by CellProfiler during the analysis using this module.
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288 You can choose from many different image formats for saving your files.
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289 This allows you to use the module as a file format converter, by loading files in their original format and then saving them in an alternate format.
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290
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291 @COMMON_HELP@
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292 ]]>
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293 </help>
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294
0
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295 <expand macro="citations" />
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296
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297 </tool>