Mercurial > repos > bgruening > cp_export_to_spreadsheet
diff export_to_spreadsheet.xml @ 3:72a7f23f3a79 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
| author | bgruening |
|---|---|
| date | Mon, 11 May 2020 07:46:16 -0400 |
| parents | c956182d4e2c |
| children | d0178bdcd00e |
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--- a/export_to_spreadsheet.xml Thu Apr 16 05:32:53 2020 -0400 +++ b/export_to_spreadsheet.xml Mon May 11 07:46:16 2020 -0400 @@ -2,6 +2,27 @@ <description>export measurements into one or more files</description> <macros> <import>macros.xml</import> + <xml name="metadata_sample_row" > + <param name="metadata_category" type="select" label="Select the metadata to use as the identifier"> + <option value="FileName">File name</option> + + <option value="Frame">Frame</option> + <option value="Height">Height</option> + <option value="MD5Digest">MD5Digest</option> + <option value="PathName">Path name</option> + + <option value="Scaling">Scaling</option> + <option value="Series">Series</option> + <option value="URL">URL</option> + <option value="Width">Width</option> + </param> + <param name="metadata_measurement" type="text" label="Measurements" > + <help> + Choose the measurement that corresponds to the identifier, such as metadata from the Metadata tool. Please see the Metadata tool for more details on metadata collection and usage. + + </help> + </param> + </xml> </macros> <expand macro="py_requirements"/> @@ -27,35 +48,39 @@ _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 + "Select the measurements to export:No\n" _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'] + _str += FOURSPACES + "Output file location:Default Output Folder\\x7C\n" create_gene = params["con_create_gene_pattern"]["create_gene_pattern"] + _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene + - 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" + #default values when create gene is no + source_sample_row = "Metadata" + image_as_id = "None" + metadata_as_id = "None" + + if create_gene == "Yes": + source_sample_row = params["con_create_gene_pattern"]["con_source_sample_row"]["select_source_sample_row_name"] + if source_sample_row == "Metadata": + metadata_as_id = params["con_create_gene_pattern"]["con_source_sample_row"]["metadata_category"] + "_" + params["con_create_gene_pattern"]["con_source_sample_row"]["metadata_measurement"] + else: + image_as_id = params["con_create_gene_pattern"]["con_source_sample_row"]["image_filename_cat"] + + _str += FOURSPACES + "Select source of sample row name:%s\n" % source_sample_row + _str += FOURSPACES + "Select the image to use as the identifier:%s\n" % image_as_id + _str += FOURSPACES + "Select the metadata to use as the identifier:%s\n" % metadata_as_id + 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 + _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 + "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"] @@ -67,13 +92,28 @@ _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params["overwrite_existing_file"] + + use_as_filename = "Yes" + 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"] + for dte in params["con_export_all_measurements"]["r_data_to_export"]: + _str += FOURSPACES + "Data to export:%s\n" % dte["data_to_export"] + _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n" + + use_as_filename = dte["con_obj_name_for_filename"]["use_as_filename"] + + if use_as_filename == "No": + file_name = dte["con_obj_name_for_filename"]["file_name"] + else: + file_name = "DATA.csv" + + _str += FOURSPACES + "File name:%s\n" % file_name + _str += FOURSPACES + "Use the object name for the file name?:%s\n" % use_as_filename return _str @@ -85,31 +125,28 @@ module_count = int(v) new_count = module_count + 1 lines[4] = k + ":%d\n" % new_count - with open("output", "w") as f: + with open("output.cppipe", "w") as f: f.writelines(lines) f.write(write_etss()) -f.close() + f.close() </configfile> </configfiles> <inputs> - <expand macro="input_pipeline_macro" /> + <expand macro="input_pipeline_param" /> <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 name="add_prefix" type="select" label="Add a prefix to file names?"> + <option value="Yes">Add prefix to the file name</option> + <option value="No">Do not add prefix to the file name</option> </param> <when value="Yes"> - <param name="filename_prefix" type="text" label="Filename prefix"/> + <param name="filename_prefix" type="text" value="MyExpt_" label="Enter the prefix to be added to the file names"/> </when> <when value="No" /> </conditional> @@ -117,89 +154,92 @@ <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?"> + <param name="add_metadata_column_to_object" display="radio" type="select" label="Add image metadata columns to your object data file?" help="'Image_Metadata_' columns are normally exported in the Image data file, but if you select 'Yes', they will also be exported with the Object data file(s)."> <option value="Yes">Yes</option> <option value="No">No</option> - </param> - <param name="represent_nan" type="select" label="Representation of Nan/Inf"> + </param> + <param name="represent_nan" type="select" label="Representation of Nan/Inf" help="CellProfiler will produce Inf or NaN values under certain rare circumstances, for instance when calculating the mean intensity of an object within a masked region of an image."> <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"> + <param name="calc_mean" type="select" display="radio" label="Calculate the per-image mean values for object measurements?" help="Select 'Yes' to calculate the population mean over all the objects in each image and save that value as an aggregate measurement in the image file."> <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"> + <param name="calc_median" type="select" display="radio" label="Calculate the per-image median values for object measurements?" help="Select 'Yes' to calculate the population median over all the objects in each image and save that value as an aggregate measurement in the image file."> <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"> + </param> + <param name="calc_standard_deviation" type="select" display="radio" label="Calculate the per-image standard deviation values for object measurements?" help="Select 'Yes' to calculate the population standard deviation over all the objects in each image and save that value as an aggregate measurement in the image file."> <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?"> + <param name="create_gene_pattern" type="select" display="radio" label="Create a GenePattern GCT file?" help="Select 'Yes' to create a GCT file compatible with GenePattern. The GCT file format is a tab-delimited text file format designed for gene expression datasets; the specifics of the format are described here. By converting your measurements into a GCT file, you can make use of GenePattern’s data visualization and clustering methods."> <option value="Yes">Yes</option> - <option value="No">No</option> + <option value="No" selected="true">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"> + <help> + <![CDATA[ + The first column of the GCT file is the unique identifier for each sample, which is ordinarily the gene name. This information may be specified in one of two ways: + <br> - Metadata: If you used the Metadata modules to add metadata to your images, you may specify a metadata tag that corresponds to the identifier for this column. + <br> - Image filename: If the gene name is not available, the image filename can be used as a surrogate identifier. + ]]> + </help> <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> + <expand macro="metadata_sample_row" /> </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> + <param name="image_filename_cat" type="text" value="None" label="Enter the name of the image to use as the identifier" help="Enter the name of the image image whose filename will be used to identify each sample row. " /> + </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?"> + <param name="export_all_measurements" type="select" display="radio" label="Export all measurement types?" help="Select 'Yes' to export every category of measurement. ExportToSpreadsheet will create one data file for each object produced in the pipeline, as well as per-image, per-experiment and object relationships, if relevant."> <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"> + <repeat name="r_data_to_export" title="another data set" min="1"> + <param name="data_to_export" type="select" label="Data to export" help="This option will writ out a file of measurements for the given category."> <option value="Image">Image</option> - <option value="Experiment">Experiement</option> + <option value="Experiment">Experiment</option> <option value="Object relationship">Object relationship</option> + <option value="Do not use">Do not use</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> + <conditional name="con_obj_name_for_filename"> + <param name="use_as_filename" type="select" display="radio" label="Use the object name for the file name?" help="Select 'Yes' to use the object name as selected above to generate a file name for the spreadsheet."> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="No"> + <param name="file_name" type="text" label="File name" /> + </when> + <when value="Yes" /> + </conditional> </repeat> - </when> + </when> <when value="Yes" /> </conditional> </inputs> <outputs> - <expand macro="output_pipeline_macro" /> + <expand macro="output_pipeline_param" /> </outputs> <tests> <test> + <!-- create gene pattern =no--> <expand macro="test_input_pipeline_param" /> <param name="delimiter" value="Tab" /> <param name="output_file_location" value="Default Output Folder" /> @@ -218,14 +258,137 @@ <conditional name="con_create_gene_pattern"> <param name="create_gene_pattern" value="No" /> </conditional> - <conditional name="con_export_all_measurements" > + <conditional name="con_export_all_measurements"> + <param name="export_all_measurements" value="Yes" /> + </conditional> + <expand macro="test_out_file" file="export_to_spreadsheet.cppipe" /> + </test> + + <test> + <!-- create gene=yes , source of sampe row name= metadata--> + <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="Yes" /> + <conditional name="con_source_sample_row"> + <param name="select_source_sample_row_name" value="Metadata" /> + <param name="metadata_category" value="FileName" /> + <param name="metadata_measurement" value="DNA" /> + </conditional> + </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" /> + <expand macro="test_out_file" file="export_to_spreadsheet_create_gene_metadata.cppipe" /> + </test> + <test> + <!-- create gene=yes , source of sampe row name= image filename, export all = no--> + <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="Yes"/> + <param name="filename_prefix" value="MyExpt_" /> + </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="Yes" /> + <conditional name="con_source_sample_row"> + <param name="select_source_sample_row_name" value="Image filename" /> + <param name="image_filename_cat" value="DNA" /> + </conditional> + </conditional> + <conditional name="con_export_all_measurements"> + <param name="export_all_measurements" value="No" /> + <repeat name="r_data_to_export"> + <param name="data_to_export" value="Image" /> + <conditional name="con_obj_name_for_filename"> + <param name="use_as_filename" value="No" /> + <param name="file_name" value="data.csv" /> + </conditional> + </repeat> + </conditional> + <expand macro="test_out_file" file="export_to_spreadsheet_create_gene_image_filename.cppipe" /> + </test> + + <test> + <!--repeat test for multiple data export. create gene=yes , source of sampe row name= image filename, export all = no--> + <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="Yes"/> + <param name="filename_prefix" value="MyExpt_" /> + </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="Yes" /> + <conditional name="con_source_sample_row"> + <param name="select_source_sample_row_name" value="Image filename" /> + <param name="image_filename_cat" value="DNA" /> + </conditional> + </conditional> + <conditional name="con_export_all_measurements"> + <param name="export_all_measurements" value="No" /> + <repeat name="r_data_to_export"> + <param name="data_to_export" value="Image" /> + <conditional name="con_obj_name_for_filename"> + <param name="use_as_filename" value="No" /> + <param name="file_name" value="data.csv" /> + </conditional> + </repeat> + <repeat name="r_data_to_export"> + <param name="data_to_export" value="Experiment" /> + <conditional name="con_obj_name_for_filename"> + <param name="use_as_filename" value="Yes" /> + </conditional> + </repeat> + </conditional> + <expand macro="test_out_file" file="export_to_spreadsheet_multi.cppipe" /> </test> </tests> - <expand macro="help" module="ExportToSpreadsheet" /> + <help> + <![CDATA[ + .. class:: infomark + + **What it does** + + This tool will convert the measurements to a comma-, tab-, or other character-delimited text format and save them in one or several files, as requested. + + @COMMON_HELP@ + ]]> + </help> + <expand macro="citations" /> </tool>