diff export_to_spreadsheet.xml @ 5:d0178bdcd00e draft default tip

"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
line wrap: on
line diff
--- 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>