Mercurial > repos > bgruening > cp_tile

annotate color_to_gray.py @ 2:443638c10c61 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:31:03 +0000
parents 878bafb411dd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import json
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5
2
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6 from cp_common_functions import (get_json_value,
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7 get_pipeline_lines,
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8 get_total_number_of_modules,
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9 INDENTATION, update_module_count,
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10 write_pipeline)
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12 MODULE_NAME = "ColorToGray"
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13 OUTPUT_FILENAME = "output.cppipe"
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16 def build_ctg_header(module_name, module_number):
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17 """Creates the first line of a module given the name and module number"""
2
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18 result = "|".join(
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19 [
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20 f"{module_name}:[module_num:{module_number}",
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21 "svn_version:\\'Unknown\\'",
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22 "variable_revision_number:4",
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23 "show_window:True",
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24 "notes:\\x5B\\'Convert the color image to grayscale.\\'\\x5D",
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25 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
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26 "enabled:True",
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27 "wants_pause:False]\n",
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28 ]
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29 )
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30 return result
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33 def build_main_block(input_params):
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34 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
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35 result = INDENTATION.join(
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36 [
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37 f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n",
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38 f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n",
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39 f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n",
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40 ]
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41 )
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42
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43 conversion_method = get_json_value(
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44 input_params, "con_conversion_method.conversion_method"
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45 )
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46
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47 image_type = get_json_value(
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48 input_params, "con_conversion_method.con_image_type.image_type"
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49 )
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50 rgb_comb_name_out = "OrigGray"
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51 combine_w_red = 1.0
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52 combine_w_green = 1.0
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53 combine_w_blue = 1.0
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54
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55 split_red = "Yes"
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56 split_green = "Yes"
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57 split_blue = "Yes"
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58 red_output_name = "OrigRed"
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59 green_output_name = "OrigGreen"
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60 blue_output_name = "OrigBlue"
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61
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62 split_hue = "Yes"
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63 split_saturation = "Yes"
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64 split_value = "Yes"
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65 hue_output_name = "OrigHue"
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66 saturation_output_name = "OrigSaturation"
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67 value_output_name = "OrigValue"
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68
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69 channel_count = 1
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70 if conversion_method == "Combine":
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71 if image_type == "RGB" or image_type == "HSV":
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72 rgb_comb_name_out = get_json_value(
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73 input_params, "con_conversion_method.name_output_image"
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74 )
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75 combine_w_red = get_json_value(
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76 input_params, "con_conversion_method.con_image_type.weight_red_channel"
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77 )
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78 combine_w_green = get_json_value(
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79 input_params,
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80 "con_conversion_method.con_image_type.weight_green_channel",
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81 )
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82 combine_w_blue = get_json_value(
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83 input_params, "con_conversion_method.con_image_type.weight_blue_channel"
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84 )
0
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85 elif conversion_method == "Split":
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86 if image_type == "RGB":
2
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87 split_red = get_json_value(
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88 input_params,
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89 "con_conversion_method.con_image_type.con_convert_red.yes_no",
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90 )
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91 red_output_name = get_json_value(
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92 input_params,
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93 "con_conversion_method.con_image_type.con_convert_red.name_output_image",
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94 )
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95 split_green = get_json_value(
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96 input_params,
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97 "con_conversion_method.con_image_type.con_convert_green.yes_no",
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98 )
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99 green_output_name = get_json_value(
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100 input_params,
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101 "con_conversion_method.con_image_type.con_convert_green.name_output_image",
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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102 )
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103 split_blue = get_json_value(
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104 input_params,
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105 "con_conversion_method.con_image_type.con_convert_blue.yes_no",
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106 )
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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107 blue_output_name = get_json_value(
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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108 input_params,
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109 "con_conversion_method.con_image_type.con_convert_blue.name_output_image",
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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110 )
0
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111 elif image_type == "HSV":
2
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112 split_hue = get_json_value(
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113 input_params,
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114 "con_conversion_method.con_image_type.con_convert_hue.yes_no",
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115 )
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116 hue_output_name = get_json_value(
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117 input_params,
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118 "con_conversion_method.con_image_type.con_convert_hue.name_output_image",
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119 )
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120 split_saturation = get_json_value(
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121 input_params,
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122 "con_conversion_method.con_image_type.con_convert_saturation.yes_no",
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123 )
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124 saturation_output_name = get_json_value(
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125 input_params,
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126 "con_conversion_method.con_image_type.con_convert_saturation.name_output_image",
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127 )
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128 split_value = get_json_value(
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129 input_params,
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130 "con_conversion_method.con_image_type.con_convert_value.yes_no",
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131 )
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132 value_output_name = get_json_value(
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133 input_params,
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134 "con_conversion_method.con_image_type.con_convert_value.name_output_image",
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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135 )
0
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136
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137 result += INDENTATION.join(
2
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138 [
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139 f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n",
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140 f"Relative weight of the red channel:{str(combine_w_red)}\n",
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141 f"Relative weight of the green channel:{str(combine_w_green)}\n",
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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142 f"Relative weight of the blue channel:{str(combine_w_blue)}\n",
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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143 f"Convert red to gray?:{split_red}\n",
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144 f"Name the output image:{red_output_name}\n",
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145 f"Convert green to gray?:{split_green}\n",
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146 f"Name the output image:{green_output_name}\n",
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147 f"Convert blue to gray?:{split_blue}\n",
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148 f"Name the output image:{blue_output_name}\n",
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149 f"Convert hue to gray?:{split_hue}\n",
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150 f"Name the output image:{hue_output_name}\n",
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151 f"Convert saturation to gray?:{split_saturation}\n",
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152 f"Name the output image:{saturation_output_name}\n",
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153 f"Convert value to gray?:{split_value}\n",
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154 f"Name the output image:{value_output_name}\n",
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155 ]
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156 )
0
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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157
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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158 channel_count = 1
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159 if image_type == "Channels":
2
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160 channels = input_params["con_conversion_method"]["con_image_type"][
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161 "rpt_channel"
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162 ]
0
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163 channel_count = len(channels)
2
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164 result += INDENTATION.join([f"{INDENTATION}Channel count:{channel_count}\n"])
0
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165
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166 for ch in channels:
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167 rel_weight_ch = 1.0
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168 image_name = "Channel1"
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169 if conversion_method == "Combine":
2
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170 rel_weight_ch = get_json_value(ch, "weight_of_channel")
0
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171 else:
2
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172 image_name = get_json_value(ch, "image_name")
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173 result += INDENTATION.join(
2
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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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177 f"Image name:{image_name}\n",
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178 ]
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179 )
0
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180 else:
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181 result += INDENTATION.join(
2
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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",
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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187 ]
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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188 )
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878bafb411dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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189 result = result.rstrip("\n")
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190 return result
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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193 if __name__ == "__main__":
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194 parser = argparse.ArgumentParser()
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443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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195 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline")
443638c10c61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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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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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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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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206 header_block = build_ctg_header(MODULE_NAME, current_module_num)
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207 main_block = build_main_block(inputs_galaxy)
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209 module_pipeline = f"\n{header_block}{main_block}\n"
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210 pipeline_lines.append(module_pipeline)
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212 write_pipeline(OUTPUT_FILENAME, pipeline_lines)