Mercurial > repos > bgruening > cp_export_to_spreadsheet
diff export_to_spreadsheet.xml @ 0:10257d6d545b 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 16:38:48 -0400 |
parents | |
children | c956182d4e2c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/export_to_spreadsheet.xml Thu Mar 26 16:38:48 2020 -0400 @@ -0,0 +1,231 @@ +<tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@"> + <description>exports 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>