Mercurial > repos > bgruening > cp_gray_to_color
view gray_to_color.xml @ 1:c72f83dbc7b5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6a3036d24b5ec074936f8f8283b7e176f6f1ce70"
author | bgruening |
---|---|
date | Thu, 09 Apr 2020 08:17:28 -0400 |
parents | d37580e3f4d0 |
children | e5870c434f28 |
line wrap: on
line source
<tool id="cp_gray_to_color" name="GrayToColor" version="@CP_VERSION@"> <description>takes grayscale images and produces a color image from them</description> <macros> <import>macros.xml</import> <xml name="rgb"> <param name="rgb_red" label="Select the image to be colored red" value="Leave this black" type="text"/> <param name="rgb_red_weight" label="Relative weight for the red image" optional="true" type="float" value="0.8"/> <param name="rgb_green" label="Select the image to be colored green" value="Leave this black" type="text"/> <param name="rgb_green_weight" label="Relative weight for the green image" optional="true" type="float" value="1.0" /> <param name="rgb_blue" label="Select the image to be colored blue" value="Leave this black" type="text"/> <param name="rgb_blue_weight" label="Relative weight for the blue image" optional="true" type="float" value="0.5"/> <param name="name_output_image" label="Name the output image" value="ColorImage" type="text"/> </xml> <xml name="cmyk"> <param name="cmyk_cyan" label="Select the image to be colored cyan" value="Leave this black" type="text"/> <param name="cmyk_cyan_weight" label="Relative weight for the cyan image" optional="true" type="float" value="0.5"/> <param name="cmyk_magenta" label="Select the image to be colored magenta" value="Leave this black" type="text"/> <param name="rgb_green_weight" label="Relative weight for the green image" optional="true" type="float" value="0.0"/> <param name="cmyk_yellow" label="Select the image to be colored yellow" value="Leave this black" type="text"/> <param name="cmyk_yellow_weight" label="Relative weight for the yellow image" optional="true" type="float" value="0.0"/> <param name="cmyk_brightness" label="Select the image that determines brightness" value="Leave this black" type="text"/> <param name="cmyk_brightness_weight" label="Relative weight for the brightness image" optional="true" type="float" value="0.5"/> <param name="name_output_image" label="Name the output image" value="ColorImage" type="text"> <expand macro="text_validator" /> </param> </xml> <xml name="stack"> <param name="name_output_image" label="Name the output image" value="ColorImage" type="text"> <expand macro="text_validator" /> </param> <repeat name="rpt_image_name" title="Add another channel"> <param name="image_name" type="text" label="Image name" > <expand macro="text_validator" /> </param> </repeat> </xml> <xml name="composite"> <param name="name_output_image" label="Name the output image" value="ColorImage" type="text"> <expand macro="text_validator" /> </param> <repeat name="rpt_image_name" title="Add another channel"> <param name="image_name" type="text" label="Image name"> <expand macro="text_validator" /> </param> <param name="color" type="color" label="Color" /> <param name="weight" type="float" label="Weight" value="0.8" min="0.0" max="1.0" /> </repeat> </xml> </macros> <expand macro="py_requirements"/> <expand macro="cmd_modules" /> <configfiles> <inputs name="inputs" /> <configfile name="script_file"> import json import sys import os FOURSPACES=@SPACES@ input_json_path = sys.argv[1] input_pipeline= sys.argv[2] params = json.load(open(input_json_path, "r")) def writegtc(): _str = "\nGrayToColor:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\\'Combine masks nuclei + nucleoli with colors\\'\\x5D|batch_state:array(\\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count color_scheme = params['con_color_scheme']['color_scheme'] rgb_blue = params['con_color_scheme']['rgb_blue'] if 'rgb_blue' in params[ 'con_color_scheme'] else 'Leave this black' rgb_blue_weight = 1.0 if params['con_color_scheme']['rgb_blue_weight'] == "" else params['con_color_scheme'][ 'rgb_blue_weight'] rgb_green = params['con_color_scheme']['rgb_green'] if 'rgb_green' in params[ 'con_color_scheme'] else 'Leave this black' rgb_green_weight = 1.0 if params['con_color_scheme']['rgb_green_weight'] == "" else params['con_color_scheme'][ 'rgb_green_weight'] rgb_red = params['con_color_scheme']['rgb_red'] if 'rgb_red' in params['con_color_scheme'] else 'Leave this black' rgb_red_weight = 1.0 if params['con_color_scheme']['rgb_red_weight'] == "" else params['con_color_scheme'][ 'rgb_red_weight'] name_output_image = params['con_color_scheme']['name_output_image'] cmyk_cyan = params['con_color_scheme']['cmyk_cyan'] if 'cmyk_cyan' in params[ 'con_color_scheme'] else 'Leave this black' if 'cmyk_cyan_weight' in params['con_color_scheme']: if params['con_color_scheme']['cmyk_cyan_weight'] == "": cmyk_cyan_weight = 1.0 else: cmyk_cyan_weight = params['con_color_scheme']['cmyk_cyan_weight'] else: cmyk_cyan_weight = 1.0 cmyk_magenta = params['con_color_scheme']['cmyk_magenta'] if 'cmyk_magenta' in params[ 'con_color_scheme'] else 'Leave this black' if 'cmyk_magenta_weight' in params['con_color_scheme']: if params['con_color_scheme']['cmyk_magenta_weight'] == "": cmyk_magenta_weight = 1.0 else: cmyk_magenta_weight = params['con_color_scheme']['cmyk_cyan_weight'] else: cmyk_magenta_weight = 1.0 cmyk_yellow = params['con_color_scheme']['cmyk_yellow'] if 'cmyk_yellow' in params[ 'con_color_scheme'] else 'Leave this black' if 'cmyk_yellow_weight' in params['con_color_scheme']: if params['con_color_scheme']['cmyk_yellow_weight'] == "": cmyk_yellow_weight = 1.0 else: cmyk_yellow_weight = params['con_color_scheme']['cmyk_yellow_weight'] else: cmyk_yellow_weight = 1.0 cmyk_brightness = params['con_color_scheme']['cmyk_brightness'] if 'cmyk_brightness' in params[ 'con_color_scheme'] else 'Leave this black' if 'cmyk_brightness_weight' in params['con_color_scheme']: if params['con_color_scheme']['cmyk_brightness_weight'] == "": cmyk_brightness_weight = 1.0 else: cmyk_brightness_weight = params['con_color_scheme']['cmyk_brightness_weight'] else: cmyk_brightness_weight = 1.0 count = len(params['con_color_scheme']['rpt_image_name']) if 'rpt_image_name' in params['con_color_scheme'] else 1 _str += FOURSPACES + "Select a color scheme:%s\n" % color_scheme _str += FOURSPACES + "Select the image to be colored red:%s\n" % rgb_red _str += FOURSPACES + "Select the image to be colored green:%s\n" % rgb_green _str += FOURSPACES + "Select the image to be colored blue:%s\n" % rgb_blue _str += FOURSPACES + "Name the output image:%s\n" % name_output_image _str += FOURSPACES + "Relative weight for the red image:%.1f\n" % rgb_red_weight _str += FOURSPACES + "Relative weight for the green image:%.1f\n" % rgb_green_weight _str += FOURSPACES + "Relative weight for the blue image:%.1f\n" % rgb_blue_weight _str += FOURSPACES + "Select the image to be colored cyan:%s\n" % cmyk_cyan _str += FOURSPACES + "Select the image to be colored magenta:%s\n" % cmyk_magenta _str += FOURSPACES + "Select the image to be colored yellow:%s\n" % cmyk_yellow _str += FOURSPACES + "Select the image that determines brightness:%s\n" % cmyk_brightness _str += FOURSPACES + "Relative weight for the cyan image:%.1f\n" % cmyk_cyan_weight _str += FOURSPACES + "Relative weight for the magenta image:%.1f\n" % cmyk_magenta_weight _str += FOURSPACES + "Relative weight for the yellow image:%.1f\n" % cmyk_yellow_weight _str += FOURSPACES + "Relative weight for the brightness image:%.1f\n" % cmyk_brightness_weight _str += FOURSPACES + "Hidden:%d\n" % count if 'rpt_image_name' in params['con_color_scheme']: for i in params['con_color_scheme']['rpt_image_name']: image_name = params['con_color_scheme']['rpt_image_name']['image_name'] if 'color' in params['con_color_scheme']['rpt_image_name']: color = params['con_color_scheme']['rpt_image_name']['color'] else: color = '#FF0000' if 'weight' in params['con_color_scheme']['rpt_image_name']: weight = params['con_color_scheme']['rpt_image_name']['weight'] else: weight = 1.0 else: image_name = 'None' color = '#FF0000' weight = 1.0 _str += FOURSPACES + "Image name:%s\n" % image_name _str += FOURSPACES + "Color:%s\n" % color _str += FOURSPACES + "Weight:%s\n" % weight return _str with open(input_pipeline) as fin: lines = fin.readlines() k, v = lines[4].strip().split(':') module_count = int(v) new_count = module_count + 1 lines[4] = k + ":%d\n" % new_count with open("output", "w") as f: f.writelines(lines) f.write(writegtc()) f.close() </configfile> </configfiles> <inputs> <expand macro="input_pipeline_macro" /> <conditional name="con_color_scheme"> <param name="color_scheme" label="Select a color scheme" type="select"> <option value="RGB">RGB</option> <option value="CMYK">CMYK</option> <option value="Stack">Stack</option> <option value="Composite">Composite</option> </param> <when value="RGB"> <expand macro="rgb" /> </when> <when value="CMYK"> <expand macro="cmyk" /> </when> <when value="Stack"> <expand macro="stack" /> </when> <when value="Composite"> <expand macro="composite" /> </when> </conditional> </inputs> <outputs> <expand macro="output_pipeline_macro" /> </outputs> <tests> <test> <expand macro="test_input_pipeline_param" /> <conditional name="con_color_scheme"> <param name="color_scheme" value="RGB" /> <param name="rgb_red" value="MaskNucleoli" /> <param name="rgb_red_weight" value="0.8" /> <param name="rgb_green" value="Leave this black" /> <param name="rgb_blue" value="MaskNuclei" /> <param name="rgb_blue_weight" value="0.5" /> <param name="name_output_image" value="CombinedMask" /> </conditional> <expand macro="test_out_file" file="gray_to_color.txt" /> </test> </tests> <expand macro="help" module="GrayToColor" /> <expand macro="citations" /> </tool>