Mercurial > repos > bgruening > cp_export_to_spreadsheet
diff export_to_spreadsheet.xml @ 5:d0178bdcd00e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
| author | bgruening |
|---|---|
| date | Fri, 26 Feb 2021 14:12:26 +0000 |
| parents | 72a7f23f3a79 |
| children | f24c370e5ea4 |
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--- a/export_to_spreadsheet.xml Sat Feb 06 10:07:37 2021 +0000 +++ b/export_to_spreadsheet.xml Fri Feb 26 14:12:26 2021 +0000 @@ -1,7 +1,8 @@ -<tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@"> +<tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@"> <description>export measurements into one or more files</description> <macros> <import>macros.xml</import> + <token name="@VERSION_SUFFIX@">1</token> <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> @@ -76,7 +77,7 @@ _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"] + export_all_measurements = "Yes" # always export all _str += FOURSPACES + "Export all measurement types?:%s\n" % export_all_measurements @@ -95,25 +96,10 @@ 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: - 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 + _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" return _str @@ -204,33 +190,7 @@ </when> <when value="No" /> </conditional> - <conditional name="con_export_all_measurements"> - <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="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">Experiment</option> - <option value="Object relationship">Object relationship</option> - <option value="Do not use">Do not use</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 value="Yes" /> - </conditional> + </inputs> <outputs> @@ -249,18 +209,12 @@ <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.cppipe" /> </test> @@ -275,9 +229,6 @@ <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" /> @@ -289,13 +240,10 @@ <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_create_gene_metadata.cppipe" /> </test> <test> - <!-- create gene=yes , source of sampe row name= image filename, export all = no--> + <!-- create gene=yes , source of sampe row name= image filename--> <expand macro="test_input_pipeline_param" /> <param name="delimiter" value="Tab" /> <param name="output_file_location" value="Default Output Folder" /> @@ -306,9 +254,6 @@ <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" /> @@ -319,21 +264,11 @@ <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--> + <!--repeat test for multiple data export. create gene=yes , source of sampe row name= image filename--> <expand macro="test_input_pipeline_param" /> <param name="delimiter" value="Tab" /> <param name="output_file_location" value="Default Output Folder" /> @@ -344,9 +279,6 @@ <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" /> @@ -357,22 +289,6 @@ <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>