Mercurial > repos > bgruening > cp_image_math
annotate image_math.py @ 0:2005f8058036 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author | bgruening |
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date | Thu, 16 Apr 2020 05:33:39 -0400 |
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children | c09dcda1143f |
rev | line source |
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0
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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1 #!/usr/bin/env python |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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2 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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3 import json |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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4 import sys |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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5 import os |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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6 import argparse |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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7 from cp_common_functions import * |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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8 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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9 MODULE_NAME = "ImageMath" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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10 OUTPUT_FILENAME = "output.cppipe" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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11 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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12 operator_map = { |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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13 "add": "Add", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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14 "subtract": "Subtract", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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15 "multiply": "Multiply", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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16 "divide": "Divide", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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17 "average": "Average", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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18 "minimum": "Minimum", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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19 "maximum": "Maximum", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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20 "invert": "Invert", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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21 "log_2": "Log transform (base 2)", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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22 "log_legacy": "Log transform (legacy)", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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23 "and": "And", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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24 "or": "Or", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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25 "not": "Not", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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26 "equals": "Equals" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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27 } |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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28 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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29 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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30 def build_main_block(input_params): |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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31 """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices""" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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32 operation = operator_map[get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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33 input_params, 'operation.operation')] |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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34 result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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35 f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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36 f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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37 f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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38 f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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39 f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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40 f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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41 f"Name the output image:{get_json_value(input_params,'name_output_image')}" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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42 ]) |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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43 return result |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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44 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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45 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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46 def build_variable_block(inputs_galaxy): |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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47 result = "" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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48 first_image_block = build_first_image_block( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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49 get_json_value(inputs_galaxy, 'operation.first_image')) |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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50 result += f"\n{first_image_block}" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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51 second_image_block = build_second_image_block( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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52 get_json_value(inputs_galaxy, 'operation.second_image')) |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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53 result += f"\n{second_image_block}" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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54 return result |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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55 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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56 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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57 def build_first_image_block(input_params): |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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58 """Creates the block of parameters for the first operator in operations""" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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59 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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60 value_select = get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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61 input_params, 'image_or_measurement_first.image_or_measurement_first') |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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62 image_name = get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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63 input_params, 'image_or_measurement_first.select_the_first_image') |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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64 value_multiply = get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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65 input_params, 'multiply_the_first_image_by') |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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66 category = get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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67 input_params, 'image_or_measurement_first.category_first.category_first') |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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68 measurement = get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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69 input_params, 'image_or_measurement_first.category_first.measurement_first') |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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70 |
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71 result = INDENTATION.join( |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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72 [f"{INDENTATION}Image or measurement?:{value_select}\n", |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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73 f"Select the first image:{image_name}\n", |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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74 f"Multiply the first image by:{value_multiply}\n", |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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75 f"Measurement:{concat_conditional(category, measurement)}" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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76 ]) |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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77 return result |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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78 |
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79 |
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80 def build_second_image_block(input_params): |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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81 """Creates the block of parameters for the second operator in binary operations""" |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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82 |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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83 value_select = get_json_value( |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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84 input_params, 'image_or_measurement_second.image_or_measurement_second') |
2005f8058036
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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85 image_name = get_json_value( |
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86 input_params, 'image_or_measurement_second.select_the_second_image') |
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87 value_multiply = get_json_value( |
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88 input_params, 'multiply_the_second_image_by') |
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89 category = get_json_value( |
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90 input_params, 'image_or_measurement_second.category_second.category_second') |
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91 measurement = get_json_value( |
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92 input_params, 'image_or_measurement_second.category_second.measurement_second') |
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93 |
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94 result = INDENTATION.join( |
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95 [f"{INDENTATION}Image or measurement?:{value_select}\n", |
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96 f"Select the second image:{image_name}\n", |
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97 f"Multiply the second image by:{value_multiply}\n", |
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98 f"Measurement:{concat_conditional(category, measurement)}" |
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99 ]) |
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100 return result |
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101 |
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102 |
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103 if __name__ == "__main__": |
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104 parser = argparse.ArgumentParser() |
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105 parser.add_argument( |
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106 '-p', '--pipeline', |
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107 help='CellProfiler pipeline' |
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108 ) |
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109 parser.add_argument( |
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110 '-i', '--inputs', |
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111 help='JSON inputs from Galaxy' |
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112 ) |
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113 args = parser.parse_args() |
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114 |
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115 pipeline_lines = get_pipeline_lines(args.pipeline) |
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116 inputs_galaxy = json.load(open(args.inputs, "r")) |
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117 |
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118 current_module_num = get_total_number_of_modules(pipeline_lines) |
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119 current_module_num += 1 |
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120 pipeline_lines = update_module_count(pipeline_lines, current_module_num) |
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121 |
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122 header_block = build_header(MODULE_NAME, current_module_num) |
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123 main_block = build_main_block(inputs_galaxy) |
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124 variable_block = build_variable_block(inputs_galaxy) |
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125 |
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126 module_pipeline = f"\n{header_block}{main_block}{variable_block}\n" |
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127 pipeline_lines.append(module_pipeline) |
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128 |
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129 write_pipeline(OUTPUT_FILENAME, pipeline_lines) |