annotate convert_objects_to_image.xml @ 2:1221c018f7be draft

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

<tool id="cp_convert_objects_to_image" name="ConvertObjectsToImage" version="@CP_VERSION@">
    <description>convert the identified objects into an image</description>
    <macros>
        <import>macros.xml</import>
    </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 writecoti():
    _str = "\nConvertObjectsToImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:1|show_window:True|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count

    _str += FOURSPACES + "Select the input objects:%s\n" % params['input_object']
    _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image']

    color_format = params['con_color_format']['color_format']

    _str += FOURSPACES + "Select the color format:%s\n" % color_format

    if color_format == "Color":
        _str += FOURSPACES + "Select the colormap:%s\n" % params['con_color_format']['color_map']
    else:
        _str += FOURSPACES + "Select the colormap:Default\n"

    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(writecoti())

f.close()
        </configfile>
    </configfiles>

    <inputs>
        <expand macro="input_pipeline_macro" />
        <param name="input_object" type="text" label="Select the input objects" />
        <param name="name_output_image" type="text" label="Name the output image">
            <expand macro="text_validator" />
        </param> 

        <conditional name="con_color_format">
            <param name="color_format" type="select" label="Select the color format">
                <option value="Color">Color</option>
                <option value="Binary (black &amp; white)">Binary (black &amp; white)</option>
                <option value="Grayscale">Grayscale</option>
                <option value="unit16">unit16</option>
                <sanitizer sanitize="false"/>
            </param>
            <when value="Binary (black &amp; white)" />
            <when value="Grayscale" />
            <when value="unit16" />
            <when value="Color">
                <param name="color_map" type="select" label="Select the colormap">
                    <option value="Default">Default</option>
                    <option value="Accent">Accent</option>
                    <option value="Blues">Blues</option>
                    <option value="BrBG">BrBG</option>
                    <option value="BuGn">BuGn</option>
                    <option value="BuPu">BuPu</option>
                    <option value="Dark2">Dark2</option>
                    <option value="GnBu">GnBu</option>
                    <option value="Greens">Greens</option>
                    <option value="Greys">Greys</option>
                    <option value="OrRd">OrRd</option>
                    <option value="Oranges">Oranges</option>
                    <option value="PRGn">PRGn</option>
                    <option value="Paired">Paired</option>
                    <option value="Pastel1">Pastel1</option>
                    <option value="Pastel2">Pastel2</option>
                    <option value="PiYG">PiYG</option>
                    <option value="PuBu">PuBu</option>
                    <option value="PuBuGn">PuBuGn</option>
                    <option value="PuOr">PuOr</option>
                    <option value="PuRd">PuRd</option>
                    <option value="Purples">Purples</option>
                    <option value="RdBu">RdBu</option>
                    <option value="RdGy">RdGy</option>
                    <option value="RdPu">RdPu</option>
                    <option value="RdYIBu">RdYIBu</option>
                    <option value="RdYiGn">RdYiGn</option>
                    <option value="Reds">Reds</option>
                    <option value="Set1">Set1</option>
                    <option value="Set2">Set2</option>
                    <option value="Set3">Set3</option>
                    <option value="Spectral">Spectral</option>
                    <option value="YIGn">YIGn</option>
                    <option value="YIGnBu">YIGnBu</option>
                    <option value="YIOrBr">YIOrBr</option>
                    <option value="YIOrRd">YIOrRd</option>
                    <option value="autumn">autumn</option>
                    <option value="binary">binary</option>
                    <option value="bone">bone</option>
                    <option value="cool">cool</option>
                    <option value="copper">copper</option>
                    <option value="flag">flag</option>
                    <option value="gist_earth">gist_earth</option>
                    <option value="gist_gray">gist_gray</option>
                    <option value="gist_heat">gist_heat</option>
                    <option value="gist_ncar">gist_ncar</option>
                    <option value="gist_rainbow">gist_rainbow</option>
                    <option value="gist_stern">gist_stern</option>
                    <option value="gist_yarg">gist_yarg</option>
                    <option value="gray">gray</option>
                    <option value="hot">hot</option>
                    <option value="hsv">hsv</option>
                    <option value="jet">jet</option>
                    <option value="pink">pink</option>
                    <option value="prism">prism</option>
                    <option value="spectral">spectral</option>
                    <option value="spring">spring</option>
                    <option value="summer">summer</option>
                    <option value="winter">winter</option>
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <expand macro="output_pipeline_macro" />
    </outputs>

    <tests>
        <test>
            <expand macro="test_input_pipeline_param" />
            <param name="input_object" value="Nuclei" />
            <param name="name_output_image" value="MaskNuclei" />
            <conditional name="con_color_format">
                <param name="color_format" value="Binary (black &amp; white)" />
            </conditional>
            <expand macro="test_out_file" file="convert_objects_to_image.txt" />
        </test>
    </tests>
    <expand macro="help" module="ConvertObjectsToImage" />
    <expand macro="citations" />
</tool>