Mercurial > repos > bgruening > cp_cellprofiler
annotate color_to_gray.py @ 7:eb6c08714244 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | bgruening |
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date | Sun, 05 Nov 2023 09:28:09 +0000 |
parents | 0e4dccaafef5 |
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rev | line source |
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5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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1 #!/usr/bin/env python |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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2 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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3 import argparse |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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4 import json |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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5 |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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6 from cp_common_functions import (get_json_value, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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7 get_pipeline_lines, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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8 get_total_number_of_modules, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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9 INDENTATION, update_module_count, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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10 write_pipeline) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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11 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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changeset
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12 MODULE_NAME = "ColorToGray" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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13 OUTPUT_FILENAME = "output.cppipe" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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14 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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15 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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16 def build_ctg_header(module_name, module_number): |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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17 """Creates the first line of a module given the name and module number""" |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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18 result = "|".join( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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19 [ |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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20 f"{module_name}:[module_num:{module_number}", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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21 "svn_version:\\'Unknown\\'", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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22 "variable_revision_number:4", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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23 "show_window:True", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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24 "notes:\\x5B\\'Convert the color image to grayscale.\\'\\x5D", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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25 "batch_state:array(\\x5B\\x5D, dtype=uint8)", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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26 "enabled:True", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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27 "wants_pause:False]\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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28 ] |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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29 ) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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30 return result |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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31 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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32 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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changeset
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33 def build_main_block(input_params): |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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34 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices""" |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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35 result = INDENTATION.join( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
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36 [ |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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37 f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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38 f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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39 f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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40 ] |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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41 ) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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42 |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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43 conversion_method = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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44 input_params, "con_conversion_method.conversion_method" |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
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45 ) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
changeset
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46 |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
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47 image_type = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
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48 input_params, "con_conversion_method.con_image_type.image_type" |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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49 ) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
changeset
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50 rgb_comb_name_out = "OrigGray" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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51 combine_w_red = 1.0 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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52 combine_w_green = 1.0 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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53 combine_w_blue = 1.0 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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54 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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55 split_red = "Yes" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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56 split_green = "Yes" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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57 split_blue = "Yes" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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58 red_output_name = "OrigRed" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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59 green_output_name = "OrigGreen" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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60 blue_output_name = "OrigBlue" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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61 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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62 split_hue = "Yes" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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63 split_saturation = "Yes" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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64 split_value = "Yes" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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65 hue_output_name = "OrigHue" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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66 saturation_output_name = "OrigSaturation" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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67 value_output_name = "OrigValue" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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68 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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69 channel_count = 1 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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70 if conversion_method == "Combine": |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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71 if image_type == "RGB" or image_type == "HSV": |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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72 rgb_comb_name_out = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
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73 input_params, "con_conversion_method.name_output_image" |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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74 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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75 combine_w_red = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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76 input_params, "con_conversion_method.con_image_type.weight_red_channel" |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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77 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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78 combine_w_green = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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79 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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80 "con_conversion_method.con_image_type.weight_green_channel", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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81 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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82 combine_w_blue = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
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83 input_params, "con_conversion_method.con_image_type.weight_blue_channel" |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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84 ) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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85 elif conversion_method == "Split": |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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diff
changeset
|
86 if image_type == "RGB": |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
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87 split_red = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
88 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
89 "con_conversion_method.con_image_type.con_convert_red.yes_no", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
90 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
91 red_output_name = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
|
92 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
|
93 "con_conversion_method.con_image_type.con_convert_red.name_output_image", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
94 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
95 split_green = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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96 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
97 "con_conversion_method.con_image_type.con_convert_green.yes_no", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
|
98 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
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99 green_output_name = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
6
diff
changeset
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100 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
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101 "con_conversion_method.con_image_type.con_convert_green.name_output_image", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
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102 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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changeset
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103 split_blue = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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changeset
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104 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
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105 "con_conversion_method.con_image_type.con_convert_blue.yes_no", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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106 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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107 blue_output_name = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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108 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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109 "con_conversion_method.con_image_type.con_convert_blue.name_output_image", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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110 ) |
5
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
changeset
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111 elif image_type == "HSV": |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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changeset
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112 split_hue = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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113 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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114 "con_conversion_method.con_image_type.con_convert_hue.yes_no", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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115 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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116 hue_output_name = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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117 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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118 "con_conversion_method.con_image_type.con_convert_hue.name_output_image", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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119 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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120 split_saturation = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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121 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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changeset
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122 "con_conversion_method.con_image_type.con_convert_saturation.yes_no", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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changeset
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123 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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124 saturation_output_name = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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125 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents:
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diff
changeset
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126 "con_conversion_method.con_image_type.con_convert_saturation.name_output_image", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
|
127 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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128 split_value = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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129 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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130 "con_conversion_method.con_image_type.con_convert_value.yes_no", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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131 ) |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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132 value_output_name = get_json_value( |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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133 input_params, |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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134 "con_conversion_method.con_image_type.con_convert_value.name_output_image", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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|
135 ) |
5
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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136 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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137 result += INDENTATION.join( |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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138 [ |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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139 f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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140 f"Relative weight of the red channel:{str(combine_w_red)}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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141 f"Relative weight of the green channel:{str(combine_w_green)}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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142 f"Relative weight of the blue channel:{str(combine_w_blue)}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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143 f"Convert red to gray?:{split_red}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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144 f"Name the output image:{red_output_name}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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145 f"Convert green to gray?:{split_green}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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146 f"Name the output image:{green_output_name}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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147 f"Convert blue to gray?:{split_blue}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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148 f"Name the output image:{blue_output_name}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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149 f"Convert hue to gray?:{split_hue}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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150 f"Name the output image:{hue_output_name}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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151 f"Convert saturation to gray?:{split_saturation}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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152 f"Name the output image:{saturation_output_name}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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153 f"Convert value to gray?:{split_value}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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154 f"Name the output image:{value_output_name}\n", |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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155 ] |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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156 ) |
5
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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157 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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158 channel_count = 1 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
changeset
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159 if image_type == "Channels": |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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160 channels = input_params["con_conversion_method"]["con_image_type"][ |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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changeset
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161 "rpt_channel" |
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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162 ] |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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163 channel_count = len(channels) |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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164 result += INDENTATION.join([f"{INDENTATION}Channel count:{channel_count}\n"]) |
5
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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165 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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166 for ch in channels: |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
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167 rel_weight_ch = 1.0 |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
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168 image_name = "Channel1" |
e917a2424690
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff
changeset
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169 if conversion_method == "Combine": |
7
eb6c08714244
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
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170 rel_weight_ch = get_json_value(ch, "weight_of_channel") |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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171 else: |
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172 image_name = get_json_value(ch, "image_name") |
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173 result += INDENTATION.join( |
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174 [ |
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175 f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n", |
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176 f"Relative weight of the channel:{str(rel_weight_ch)}\n", |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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177 f"Image name:{image_name}\n", |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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178 ] |
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179 ) |
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180 else: |
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181 result += INDENTATION.join( |
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182 [ |
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183 f"{INDENTATION}Channel count:{channel_count}\n", |
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184 "Channel number:Red\\x3A 1\n", |
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185 "Relative weight of the channel:1.0\n", |
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186 "Image name:Channel1\n", |
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187 ] |
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188 ) |
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189 result = result.rstrip("\n") |
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190 return result |
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191 |
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192 |
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193 if __name__ == "__main__": |
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194 parser = argparse.ArgumentParser() |
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195 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline") |
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196 parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy") |
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197 args = parser.parse_args() |
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198 |
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199 pipeline_lines = get_pipeline_lines(args.pipeline) |
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200 inputs_galaxy = json.load(open(args.inputs, "r")) |
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201 |
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202 current_module_num = get_total_number_of_modules(pipeline_lines) |
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203 current_module_num += 1 |
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204 pipeline_lines = update_module_count(pipeline_lines, current_module_num) |
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205 |
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206 header_block = build_ctg_header(MODULE_NAME, current_module_num) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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207 main_block = build_main_block(inputs_galaxy) |
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208 |
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209 module_pipeline = f"\n{header_block}{main_block}\n" |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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210 pipeline_lines.append(module_pipeline) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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211 |
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212 write_pipeline(OUTPUT_FILENAME, pipeline_lines) |