Mercurial > repos > bgruening > cp_measure_object_size_shape
view measure_object_size_shape.xml @ 0:eba2ec72f967 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author | bgruening |
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date | Thu, 26 Mar 2020 17:45:13 -0400 |
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children | 5ef26243a4a5 |
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<tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@"> <description>measures several area and shape features of identified 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 writemoss(): _str = "\nMeasureObjectSizeShape:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:1|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count for obj in params['rpt_object']: _str += FOURSPACES + "Select objects to measure:%s\n" % obj['objects_to_measure'] _str += FOURSPACES + "Calculate the Zernike features?:%s\n" % params['zernike_feature'] 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(writemoss()) f.close() </configfile> </configfiles> <inputs> <expand macro="input_pipeline_macro" /> <repeat name="rpt_object" title="Add another object"> <param name="objects_to_measure" label="Select objects to measure" type="text" > <expand macro="text_validator" /> </param> </repeat> <param name="zernike_feature" type="select" display="radio" label="Calculate the Zernike features?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> </inputs> <outputs> <expand macro="output_pipeline_macro" /> </outputs> <tests> <test> <expand macro="test_input_pipeline_param" /> <repeat name="rpt_object"> <param name="objects_to_measure" value="Nuclei" /> </repeat> <repeat name="rpt_object"> <param name="objects_to_measure" value="Nucleoli" /> </repeat> <param name="zernike_feature" value="Yes" /> <expand macro="test_out_file" file="measure_object_size_shape.txt" /> </test> </tests> <expand macro="help" module="MeasureObjectSizeShape" /> <expand macro="citations" /> </tool>