annotate measure_image_area_occupied.xml @ 2:534ed7b8ca34 draft

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

<tool id="cp_measure_image_area_occupied" name="MeasureImageAreaOccupied" version="@CP_VERSION@">
    <description>measure the area in an image occupied by objects</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 writemiao():
    _str = "\nMeasureImageAreaOccupied:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count

    hidden = len(params['rpt_area'])

    _str += FOURSPACES + "Hidden:%d\n" % hidden

    for area in params['rpt_area']:
        _str += FOURSPACES + "Measure the area occupied in a binary image, or in objects?:%s\n" % area['con_area']['objects_or_image']

        obj_flag = area['con_area']['objects_or_image']

        if obj_flag == "Objects":
            _str += FOURSPACES + "Select objects to measure:%s\n" % area['con_area']['objects_to_measure']
            _str += FOURSPACES + "Select a binary image to measure:None\n"
        else:
            _str += FOURSPACES + "Select objects to measure:None\n"
            _str += FOURSPACES + "Select a binary image to measure:%s\n" % area['con_area']['image_to_measure']
            
    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(writemiao())

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

    <inputs>
        <expand macro="input_pipeline_macro" />
        <repeat name="rpt_area" title="Add another area">
            <conditional name="con_area">
                <param name="objects_or_image" label="Measure the area occupied in a binary image, or in objects?" type="select">
                    <option value="Binary image">Binary image</option>
                    <option value="Objects">Objects</option>
                </param>
                <when value="Objects">
                    <param name="objects_to_measure" label="Select objects to measure" type="text">
                        <expand macro="text_validator" />
                    </param>
                </when>
                <when value="Binary image">
                    <param name="image_to_measure" label="Select a binary image to measure" type="text">
                        <expand macro="text_validator" />
                    </param>
                </when>
            </conditional>
        </repeat>
  </inputs>

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

    <tests>
        <test>
            <expand macro="test_input_pipeline_param" />
            <repeat name="rpt_area">
                <conditional name="con_area">
                    <param name="objects_or_image" value="Objects" />
                    <param name="objects_to_measure" value="Nuclei" />
                </conditional>
            </repeat>
            <repeat name="rpt_area">
                <conditional name="con_area">
                    <param name="objects_or_image" value="Objects" />
                    <param name="objects_to_measure" value="Nucleoli" />
                </conditional>
            </repeat>
            <expand macro="test_out_file" file="measure_image_area_occupied.txt" />
        </test>
    </tests>

    <expand macro="help" module="MeasureImageAreaOccupied" />
    <expand macro="citations" />
</tool>