annotate gray_to_color.xml @ 2:e5870c434f28 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"

<tool id="cp_gray_to_color" name="GrayToColor" version="@CP_VERSION@">
    <description>take 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>