Mercurial > repos > bgruening > cp_export_to_spreadsheet
view export_to_spreadsheet.xml @ 2:c956182d4e2c draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author | bgruening |
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date | Thu, 16 Apr 2020 05:32:53 -0400 |
parents | 10257d6d545b |
children | 72a7f23f3a79 |
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<tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@"> <description>export measurements into one or more files</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 write_etss(): _str = "\nExportToSpreadsheet:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:12|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 column delimiter:%s\n" % params["delimiter"] _str += FOURSPACES + "Add image metadata columns to your object data file?:%s\n" % params["add_metadata_column_to_object"] measurement = params["con_measurement_export"] _str += FOURSPACES + "Select the measurements to export:%s\n" % measurement['export_measurement'] _str += FOURSPACES + "Calculate the per-image mean values for object measurements?:%s\n" % params['calc_mean'] _str += FOURSPACES + "Calculate the per-image median values for object measurements?:%s\n" % params['calc_median'] _str += FOURSPACES + "Calculate the per-image standard deviation values for object measurements?:%s\n" % params['calc_standard_deviation'] _str += FOURSPACES + "Output file location:%s\\x7C\n" % params['output_file_location'] create_gene = params["con_create_gene_pattern"]["create_gene_pattern"] if create_gene == "No": _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene _str += FOURSPACES + "Select source of sample row name:Metadata\n" _str += FOURSPACES + "Select the image to use as the identifier:None\n" _str += FOURSPACES + "Select the metadata to use as the identifier:None\n" else: _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene _str += FOURSPACES + "Select the image to use as the identifier:None\n" _str += FOURSPACES + "Select the metadata to use as the identifier:None\n" export_all_measurements = params["con_export_all_measurements"]["export_all_measurements"] if export_all_measurements == "Yes": _str += FOURSPACES + "Export all measurement types?:%s\n" % export_all_measurements if 'select_measurements' in params['con_measurement_export']: _str += FOURSPACES + "Press button to select measurements:%s\n" % params['con_measurement_export']['select_measurements'] else: _str += FOURSPACES + "Press button to select measurements:\n" _str += FOURSPACES + "Representation of Nan/Inf:%s\n" % params["represent_nan"] _str += FOURSPACES + "Add a prefix to file names?:%s\n" % params["con_prefix"]["add_prefix"] if "filename_prefix" in params["con_prefix"]: _str += FOURSPACES + "Filename prefix:%s\n" % params["con_prefix"]["filename_prefix"] else: _str += FOURSPACES + "Filename prefix:MyPrefix_\n" _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params["overwrite_existing_file"] if export_all_measurements == "Yes": _str += FOURSPACES + "Data to export:Do not use\n" _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n" _str += FOURSPACES + "File name:DATA.csv\n" _str += FOURSPACES + "Use the object name for the file name?:Yes\n" else: _str += FOURSPACES + "Data to export:%s\n" % params["con_export_all_measurements"]["data_to_export"] 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(write_etss()) f.close() </configfile> </configfiles> <inputs> <expand macro="input_pipeline_macro" /> <param name="delimiter" type="select" label="Select the column delimiter"> <option value="Comma (",")">Comma (",")</option> <option value="Tab">Tab</option> <sanitizer sanitize="false"/> </param> <param name="output_file_location" type="select" label="Output file location"> <option value="Default Output Folder"/> </param> <conditional name="con_prefix"> <param name="add_prefix" type="select" display="radio" label="Add a prefix to file names?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <when value="Yes"> <param name="filename_prefix" type="text" label="Filename prefix"/> </when> <when value="No" /> </conditional> <param name="overwrite_existing_file" display="radio" type="select" label="Overwrite existing files without warning?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <param name="add_metadata_column_to_object" display="radio" type="select" label="Add image metadata columns to your object data file?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <param name="represent_nan" type="select" label="Representation of Nan/Inf"> <option value="NaN">NaN</option> <option value="Null">Null</option> </param> <conditional name="con_measurement_export"> <param name="export_measurement" type="select" display="radio" label="Select the measurements to export"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <when value="Yes"> <param name="select_measurement" type="text" label="Select measurements"/> </when> <when value="No" /> </conditional> <param name="calc_mean" type="select" display="radio" label="Calculate the per-image mean values for object measurments"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <param name="calc_median" type="select" display="radio" label="Calculate the per-image median values for object measurments"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <param name="calc_standard_deviation" type="select" display="radio" label="Calculate the per-image standard deviation values for object measurments"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <conditional name="con_create_gene_pattern"> <param name="create_gene_pattern" type="select" display="radio" label="Create a GenePattern GCT file?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <when value="Yes"> <conditional name="con_source_sample_row"> <param name="select_source_sample_row_name" type="select" label="Select source of sample row name"> <option value="Metadata">Metadata</option> <option value="Image filename">Image filename</option> </param> <when value="Metadata"> <param name="metadata_cat" type="select" label="Select the metadata to use as the indentifier"> <option value="AreaOccupied">AreaOccupied</option> </param> </when> <when value="Image filename"> <param name="image_filename_cat" type="select" label="Select the image to use as the indentifier"> <option value="None">None</option> </param> </when> </conditional> </when> <when value="No" /> </conditional> <conditional name="con_export_all_measurements"> <param name="export_all_measurements" type="select" display="radio" label="Export all measuremnt types?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> <when value="No"> <repeat name="r_data_to_export" title="Add another data set"> <param name="data_to_export" type="select" label="Data to export"> <option value="Image">Image</option> <option value="Experiment">Experiement</option> <option value="Object relationship">Object relationship</option> </param> <param name="use_as_filename" type="select" display="radio" label="Use the object name for the file name?"> <option value="Yes">Yes</option> <option value="No">No</option> </param> </repeat> </when> <when value="Yes" /> </conditional> </inputs> <outputs> <expand macro="output_pipeline_macro" /> </outputs> <tests> <test> <expand macro="test_input_pipeline_param" /> <param name="delimiter" value="Tab" /> <param name="output_file_location" value="Default Output Folder" /> <conditional name="con_prefix"> <param name="add_prefix" value="No"/> </conditional> <param name="overwrite_existing_file" value="Yes" /> <param name="add_metadata_column_to_object" value="Yes" /> <param name="represent_nan" value="NaN" /> <conditional name="con_measurement_export"> <param name="export_measurement" value="No" /> </conditional> <param name="calc_mean" value="Yes" /> <param name="calc_median" value="Yes" /> <param name="calc_standard_deviation" value="Yes" /> <conditional name="con_create_gene_pattern"> <param name="create_gene_pattern" value="No" /> </conditional> <conditional name="con_export_all_measurements" > <param name="export_all_measurements" value="Yes" /> </conditional> <expand macro="test_out_file" file="export_to_spreadsheet.txt" /> </test> </tests> <expand macro="help" module="ExportToSpreadsheet" /> <expand macro="citations" /> </tool>