Mercurial > repos > bgruening > cp_convert_objects_to_image
diff convert_objects_to_image.xml @ 0:d9fa2e6fae97 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
| author | bgruening |
|---|---|
| date | Thu, 26 Mar 2020 16:17:05 -0400 |
| parents | |
| children | 1221c018f7be |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert_objects_to_image.xml Thu Mar 26 16:17:05 2020 -0400 @@ -0,0 +1,157 @@ +<tool id="cp_convert_objects_to_image" name="ConvertObjectsToImage" version="@CP_VERSION@"> + <description>converts 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 & white)">Binary (black & white)</option> + <option value="Grayscale">Grayscale</option> + <option value="unit16">unit16</option> + <sanitizer sanitize="false"/> + </param> + <when value="Binary (black & 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 & white)" /> + </conditional> + <expand macro="test_out_file" file="convert_objects_to_image.txt" /> + </test> + </tests> + <expand macro="help" module="ConvertObjectsToImage" /> + <expand macro="citations" /> +</tool>