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comparison export_to_spreadsheet.xml @ 3:72a7f23f3a79 draft

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"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
comparison
equal deleted inserted replaced
2:c956182d4e2c 3:72a7f23f3a79
1 <tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@"> 1 <tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@">
2 <description>export measurements into one or more files</description> 2 <description>export measurements into one or more files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="metadata_sample_row" >
6 <param name="metadata_category" type="select" label="Select the metadata to use as the identifier">
7 <option value="FileName">File name</option>
8
9 <option value="Frame">Frame</option>
10 <option value="Height">Height</option>
11 <option value="MD5Digest">MD5Digest</option>
12 <option value="PathName">Path name</option>
13
14 <option value="Scaling">Scaling</option>
15 <option value="Series">Series</option>
16 <option value="URL">URL</option>
17 <option value="Width">Width</option>
18 </param>
19 <param name="metadata_measurement" type="text" label="Measurements" >
20 <help>
21 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.
22
23 </help>
24 </param>
25 </xml>
5 </macros> 26 </macros>
6 27
7 <expand macro="py_requirements"/> 28 <expand macro="py_requirements"/>
8 <expand macro="cmd_modules" /> 29 <expand macro="cmd_modules" />
9 30
25 def write_etss(): 46 def write_etss():
26 _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 47 _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
27 _str += FOURSPACES + "Select the column delimiter:%s\n" % params["delimiter"] 48 _str += FOURSPACES + "Select the column delimiter:%s\n" % params["delimiter"]
28 _str += FOURSPACES + "Add image metadata columns to your object data file?:%s\n" % params["add_metadata_column_to_object"] 49 _str += FOURSPACES + "Add image metadata columns to your object data file?:%s\n" % params["add_metadata_column_to_object"]
29 50
30 measurement = params["con_measurement_export"] 51
31 52 _str += FOURSPACES + "Select the measurements to export:No\n"
32 _str += FOURSPACES + "Select the measurements to export:%s\n" % measurement['export_measurement']
33 _str += FOURSPACES + "Calculate the per-image mean values for object measurements?:%s\n" % params['calc_mean'] 53 _str += FOURSPACES + "Calculate the per-image mean values for object measurements?:%s\n" % params['calc_mean']
34 _str += FOURSPACES + "Calculate the per-image median values for object measurements?:%s\n" % params['calc_median'] 54 _str += FOURSPACES + "Calculate the per-image median values for object measurements?:%s\n" % params['calc_median']
35 _str += FOURSPACES + "Calculate the per-image standard deviation values for object measurements?:%s\n" % params['calc_standard_deviation'] 55 _str += FOURSPACES + "Calculate the per-image standard deviation values for object measurements?:%s\n" % params['calc_standard_deviation']
36 _str += FOURSPACES + "Output file location:%s\\x7C\n" % params['output_file_location'] 56 _str += FOURSPACES + "Output file location:Default Output Folder\\x7C\n"
37 57
38 create_gene = params["con_create_gene_pattern"]["create_gene_pattern"] 58 create_gene = params["con_create_gene_pattern"]["create_gene_pattern"]
39 59 _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene
40 if create_gene == "No": 60
41 _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene 61
42 _str += FOURSPACES + "Select source of sample row name:Metadata\n" 62 #default values when create gene is no
43 _str += FOURSPACES + "Select the image to use as the identifier:None\n" 63 source_sample_row = "Metadata"
44 _str += FOURSPACES + "Select the metadata to use as the identifier:None\n" 64 image_as_id = "None"
45 else: 65 metadata_as_id = "None"
46 _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene 66
47 _str += FOURSPACES + "Select the image to use as the identifier:None\n" 67 if create_gene == "Yes":
48 _str += FOURSPACES + "Select the metadata to use as the identifier:None\n" 68 source_sample_row = params["con_create_gene_pattern"]["con_source_sample_row"]["select_source_sample_row_name"]
69 if source_sample_row == "Metadata":
70 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"]
71 else:
72 image_as_id = params["con_create_gene_pattern"]["con_source_sample_row"]["image_filename_cat"]
73
74 _str += FOURSPACES + "Select source of sample row name:%s\n" % source_sample_row
75 _str += FOURSPACES + "Select the image to use as the identifier:%s\n" % image_as_id
76 _str += FOURSPACES + "Select the metadata to use as the identifier:%s\n" % metadata_as_id
77
49 78
50 export_all_measurements = params["con_export_all_measurements"]["export_all_measurements"] 79 export_all_measurements = params["con_export_all_measurements"]["export_all_measurements"]
51 80
52 if export_all_measurements == "Yes": 81 _str += FOURSPACES + "Export all measurement types?:%s\n" % export_all_measurements
53 _str += FOURSPACES + "Export all measurement types?:%s\n" % export_all_measurements 82
54 83 _str += FOURSPACES + "Press button to select measurements:\n"
55 if 'select_measurements' in params['con_measurement_export']:
56 _str += FOURSPACES + "Press button to select measurements:%s\n" % params['con_measurement_export']['select_measurements']
57 else:
58 _str += FOURSPACES + "Press button to select measurements:\n"
59 84
60 _str += FOURSPACES + "Representation of Nan/Inf:%s\n" % params["represent_nan"] 85 _str += FOURSPACES + "Representation of Nan/Inf:%s\n" % params["represent_nan"]
61 _str += FOURSPACES + "Add a prefix to file names?:%s\n" % params["con_prefix"]["add_prefix"] 86 _str += FOURSPACES + "Add a prefix to file names?:%s\n" % params["con_prefix"]["add_prefix"]
62 87
63 if "filename_prefix" in params["con_prefix"]: 88 if "filename_prefix" in params["con_prefix"]:
64 _str += FOURSPACES + "Filename prefix:%s\n" % params["con_prefix"]["filename_prefix"] 89 _str += FOURSPACES + "Filename prefix:%s\n" % params["con_prefix"]["filename_prefix"]
65 else: 90 else:
66 _str += FOURSPACES + "Filename prefix:MyPrefix_\n" 91 _str += FOURSPACES + "Filename prefix:MyPrefix_\n"
67 92
68 _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params["overwrite_existing_file"] 93 _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params["overwrite_existing_file"]
94
95
96 use_as_filename = "Yes"
69 97
70 if export_all_measurements == "Yes": 98 if export_all_measurements == "Yes":
71 _str += FOURSPACES + "Data to export:Do not use\n" 99 _str += FOURSPACES + "Data to export:Do not use\n"
72 _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n" 100 _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n"
73 _str += FOURSPACES + "File name:DATA.csv\n" 101 _str += FOURSPACES + "File name:DATA.csv\n"
74 _str += FOURSPACES + "Use the object name for the file name?:Yes\n" 102 _str += FOURSPACES + "Use the object name for the file name?:Yes\n"
75 else: 103 else:
76 _str += FOURSPACES + "Data to export:%s\n" % params["con_export_all_measurements"]["data_to_export"] 104 for dte in params["con_export_all_measurements"]["r_data_to_export"]:
105 _str += FOURSPACES + "Data to export:%s\n" % dte["data_to_export"]
106 _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n"
107
108 use_as_filename = dte["con_obj_name_for_filename"]["use_as_filename"]
109
110 if use_as_filename == "No":
111 file_name = dte["con_obj_name_for_filename"]["file_name"]
112 else:
113 file_name = "DATA.csv"
114
115 _str += FOURSPACES + "File name:%s\n" % file_name
116 _str += FOURSPACES + "Use the object name for the file name?:%s\n" % use_as_filename
77 117
78 return _str 118 return _str
79 119
80 with open(input_pipeline) as fin: 120 with open(input_pipeline) as fin:
81 lines = fin.readlines() 121 lines = fin.readlines()
83 k, v = lines[4].strip().split(':') 123 k, v = lines[4].strip().split(':')
84 124
85 module_count = int(v) 125 module_count = int(v)
86 new_count = module_count + 1 126 new_count = module_count + 1
87 lines[4] = k + ":%d\n" % new_count 127 lines[4] = k + ":%d\n" % new_count
88 with open("output", "w") as f: 128 with open("output.cppipe", "w") as f:
89 f.writelines(lines) 129 f.writelines(lines)
90 f.write(write_etss()) 130 f.write(write_etss())
91 131
92 f.close() 132 f.close()
93 </configfile> 133 </configfile>
94 </configfiles> 134 </configfiles>
95 135
96 <inputs> 136 <inputs>
97 <expand macro="input_pipeline_macro" /> 137 <expand macro="input_pipeline_param" />
98 <param name="delimiter" type="select" label="Select the column delimiter"> 138 <param name="delimiter" type="select" label="Select the column delimiter">
99 <option value="Comma (&quot;,&quot;)">Comma (",")</option> 139 <option value="Comma (&quot;,&quot;)">Comma (",")</option>
100 <option value="Tab">Tab</option> 140 <option value="Tab">Tab</option>
101 <sanitizer sanitize="false"/> 141 <sanitizer sanitize="false"/>
102 </param> 142 </param>
103 <param name="output_file_location" type="select" label="Output file location">
104 <option value="Default Output Folder"/>
105 </param>
106 <conditional name="con_prefix"> 143 <conditional name="con_prefix">
107 <param name="add_prefix" type="select" display="radio" label="Add a prefix to file names?"> 144 <param name="add_prefix" type="select" label="Add a prefix to file names?">
108 <option value="Yes">Yes</option> 145 <option value="Yes">Add prefix to the file name</option>
109 <option value="No">No</option> 146 <option value="No">Do not add prefix to the file name</option>
110 </param> 147 </param>
111 <when value="Yes"> 148 <when value="Yes">
112 <param name="filename_prefix" type="text" label="Filename prefix"/> 149 <param name="filename_prefix" type="text" value="MyExpt_" label="Enter the prefix to be added to the file names"/>
113 </when> 150 </when>
114 <when value="No" /> 151 <when value="No" />
115 </conditional> 152 </conditional>
116 <param name="overwrite_existing_file" display="radio" type="select" label="Overwrite existing files without warning?"> 153 <param name="overwrite_existing_file" display="radio" type="select" label="Overwrite existing files without warning?">
117 <option value="Yes">Yes</option> 154 <option value="Yes">Yes</option>
118 <option value="No">No</option> 155 <option value="No">No</option>
119 </param> 156 </param>
120 <param name="add_metadata_column_to_object" display="radio" type="select" label="Add image metadata columns to your object data file?"> 157 <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).">
121 <option value="Yes">Yes</option> 158 <option value="Yes">Yes</option>
122 <option value="No">No</option> 159 <option value="No">No</option>
123 </param> 160 </param>
124 <param name="represent_nan" type="select" label="Representation of Nan/Inf"> 161 <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.">
125 <option value="NaN">NaN</option> 162 <option value="NaN">NaN</option>
126 <option value="Null">Null</option> 163 <option value="Null">Null</option>
127 </param> 164 </param>
128 <conditional name="con_measurement_export"> 165 <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.">
129 <param name="export_measurement" type="select" display="radio" label="Select the measurements to export"> 166 <option value="Yes">Yes</option>
167 <option value="No">No</option>
168 </param>
169 <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.">
170 <option value="Yes">Yes</option>
171 <option value="No">No</option>
172 </param>
173 <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.">
174 <option value="Yes">Yes</option>
175 <option value="No">No</option>
176 </param>
177 <conditional name="con_create_gene_pattern">
178 <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.">
130 <option value="Yes">Yes</option> 179 <option value="Yes">Yes</option>
131 <option value="No">No</option> 180 <option value="No" selected="true">No</option>
132 </param>
133 <when value="Yes">
134 <param name="select_measurement" type="text" label="Select measurements"/>
135 </when>
136 <when value="No" />
137 </conditional>
138 <param name="calc_mean" type="select" display="radio" label="Calculate the per-image mean values for object measurments">
139 <option value="Yes">Yes</option>
140 <option value="No">No</option>
141 </param>
142 <param name="calc_median" type="select" display="radio" label="Calculate the per-image median values for object measurments">
143 <option value="Yes">Yes</option>
144 <option value="No">No</option>
145 </param>
146 <param name="calc_standard_deviation" type="select" display="radio" label="Calculate the per-image standard deviation values for object measurments">
147 <option value="Yes">Yes</option>
148 <option value="No">No</option>
149 </param>
150 <conditional name="con_create_gene_pattern">
151 <param name="create_gene_pattern" type="select" display="radio" label="Create a GenePattern GCT file?">
152 <option value="Yes">Yes</option>
153 <option value="No">No</option>
154 </param> 181 </param>
155 <when value="Yes"> 182 <when value="Yes">
156 <conditional name="con_source_sample_row"> 183 <conditional name="con_source_sample_row">
157 <param name="select_source_sample_row_name" type="select" label="Select source of sample row name"> 184 <param name="select_source_sample_row_name" type="select" label="Select source of sample row name">
185 <help>
186 <![CDATA[
187 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:
188 <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.
189 <br> - Image filename: If the gene name is not available, the image filename can be used as a surrogate identifier.
190 ]]>
191 </help>
158 <option value="Metadata">Metadata</option> 192 <option value="Metadata">Metadata</option>
159 <option value="Image filename">Image filename</option> 193 <option value="Image filename">Image filename</option>
160 </param> 194 </param>
195
161 <when value="Metadata"> 196 <when value="Metadata">
162 <param name="metadata_cat" type="select" label="Select the metadata to use as the indentifier"> 197 <expand macro="metadata_sample_row" />
163 <option value="AreaOccupied">AreaOccupied</option>
164 </param>
165 </when> 198 </when>
166 <when value="Image filename"> 199 <when value="Image filename">
167 <param name="image_filename_cat" type="select" label="Select the image to use as the indentifier"> 200 <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. " />
168 <option value="None">None</option> 201
169 </param>
170 </when> 202 </when>
171 </conditional> 203 </conditional>
172 </when> 204 </when>
173 <when value="No" /> 205 <when value="No" />
174 </conditional> 206 </conditional>
175 <conditional name="con_export_all_measurements"> 207 <conditional name="con_export_all_measurements">
176 <param name="export_all_measurements" type="select" display="radio" label="Export all measuremnt types?"> 208 <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.">
177 <option value="Yes">Yes</option> 209 <option value="Yes">Yes</option>
178 <option value="No">No</option> 210 <option value="No">No</option>
179 </param> 211 </param>
180 <when value="No"> 212 <when value="No">
181 <repeat name="r_data_to_export" title="Add another data set"> 213 <repeat name="r_data_to_export" title="another data set" min="1">
182 <param name="data_to_export" type="select" label="Data to export"> 214 <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.">
183 <option value="Image">Image</option> 215 <option value="Image">Image</option>
184 <option value="Experiment">Experiement</option> 216 <option value="Experiment">Experiment</option>
185 <option value="Object relationship">Object relationship</option> 217 <option value="Object relationship">Object relationship</option>
218 <option value="Do not use">Do not use</option>
186 </param> 219 </param>
187 <param name="use_as_filename" type="select" display="radio" label="Use the object name for the file name?"> 220 <conditional name="con_obj_name_for_filename">
188 <option value="Yes">Yes</option> 221 <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.">
189 <option value="No">No</option> 222 <option value="Yes">Yes</option>
190 </param> 223 <option value="No">No</option>
224 </param>
225 <when value="No">
226 <param name="file_name" type="text" label="File name" />
227 </when>
228 <when value="Yes" />
229 </conditional>
191 </repeat> 230 </repeat>
192 </when> 231 </when>
193 <when value="Yes" /> 232 <when value="Yes" />
194 </conditional> 233 </conditional>
195 </inputs> 234 </inputs>
196 235
197 <outputs> 236 <outputs>
198 <expand macro="output_pipeline_macro" /> 237 <expand macro="output_pipeline_param" />
199 </outputs> 238 </outputs>
200 239
201 <tests> 240 <tests>
202 <test> 241 <test>
242 <!-- create gene pattern =no-->
203 <expand macro="test_input_pipeline_param" /> 243 <expand macro="test_input_pipeline_param" />
204 <param name="delimiter" value="Tab" /> 244 <param name="delimiter" value="Tab" />
205 <param name="output_file_location" value="Default Output Folder" /> 245 <param name="output_file_location" value="Default Output Folder" />
206 <conditional name="con_prefix"> 246 <conditional name="con_prefix">
207 <param name="add_prefix" value="No"/> 247 <param name="add_prefix" value="No"/>
216 <param name="calc_median" value="Yes" /> 256 <param name="calc_median" value="Yes" />
217 <param name="calc_standard_deviation" value="Yes" /> 257 <param name="calc_standard_deviation" value="Yes" />
218 <conditional name="con_create_gene_pattern"> 258 <conditional name="con_create_gene_pattern">
219 <param name="create_gene_pattern" value="No" /> 259 <param name="create_gene_pattern" value="No" />
220 </conditional> 260 </conditional>
221 <conditional name="con_export_all_measurements" > 261 <conditional name="con_export_all_measurements">
222 <param name="export_all_measurements" value="Yes" /> 262 <param name="export_all_measurements" value="Yes" />
223 </conditional> 263 </conditional>
224 <expand macro="test_out_file" file="export_to_spreadsheet.txt" /> 264 <expand macro="test_out_file" file="export_to_spreadsheet.cppipe" />
265 </test>
266
267 <test>
268 <!-- create gene=yes , source of sampe row name= metadata-->
269 <expand macro="test_input_pipeline_param" />
270 <param name="delimiter" value="Tab" />
271 <param name="output_file_location" value="Default Output Folder" />
272 <conditional name="con_prefix">
273 <param name="add_prefix" value="No"/>
274 </conditional>
275 <param name="overwrite_existing_file" value="Yes" />
276 <param name="add_metadata_column_to_object" value="Yes" />
277 <param name="represent_nan" value="NaN" />
278 <conditional name="con_measurement_export">
279 <param name="export_measurement" value="No" />
280 </conditional>
281 <param name="calc_mean" value="Yes" />
282 <param name="calc_median" value="Yes" />
283 <param name="calc_standard_deviation" value="Yes" />
284 <conditional name="con_create_gene_pattern">
285 <param name="create_gene_pattern" value="Yes" />
286 <conditional name="con_source_sample_row">
287 <param name="select_source_sample_row_name" value="Metadata" />
288 <param name="metadata_category" value="FileName" />
289 <param name="metadata_measurement" value="DNA" />
290 </conditional>
291 </conditional>
292 <conditional name="con_export_all_measurements">
293 <param name="export_all_measurements" value="Yes" />
294 </conditional>
295 <expand macro="test_out_file" file="export_to_spreadsheet_create_gene_metadata.cppipe" />
296 </test>
297 <test>
298 <!-- create gene=yes , source of sampe row name= image filename, export all = no-->
299 <expand macro="test_input_pipeline_param" />
300 <param name="delimiter" value="Tab" />
301 <param name="output_file_location" value="Default Output Folder" />
302 <conditional name="con_prefix">
303 <param name="add_prefix" value="Yes"/>
304 <param name="filename_prefix" value="MyExpt_" />
305 </conditional>
306 <param name="overwrite_existing_file" value="Yes" />
307 <param name="add_metadata_column_to_object" value="Yes" />
308 <param name="represent_nan" value="NaN" />
309 <conditional name="con_measurement_export">
310 <param name="export_measurement" value="No" />
311 </conditional>
312 <param name="calc_mean" value="Yes" />
313 <param name="calc_median" value="Yes" />
314 <param name="calc_standard_deviation" value="Yes" />
315 <conditional name="con_create_gene_pattern">
316 <param name="create_gene_pattern" value="Yes" />
317 <conditional name="con_source_sample_row">
318 <param name="select_source_sample_row_name" value="Image filename" />
319 <param name="image_filename_cat" value="DNA" />
320 </conditional>
321 </conditional>
322 <conditional name="con_export_all_measurements">
323 <param name="export_all_measurements" value="No" />
324 <repeat name="r_data_to_export">
325 <param name="data_to_export" value="Image" />
326 <conditional name="con_obj_name_for_filename">
327 <param name="use_as_filename" value="No" />
328 <param name="file_name" value="data.csv" />
329 </conditional>
330 </repeat>
331 </conditional>
332 <expand macro="test_out_file" file="export_to_spreadsheet_create_gene_image_filename.cppipe" />
333 </test>
334
335 <test>
336 <!--repeat test for multiple data export. create gene=yes , source of sampe row name= image filename, export all = no-->
337 <expand macro="test_input_pipeline_param" />
338 <param name="delimiter" value="Tab" />
339 <param name="output_file_location" value="Default Output Folder" />
340 <conditional name="con_prefix">
341 <param name="add_prefix" value="Yes"/>
342 <param name="filename_prefix" value="MyExpt_" />
343 </conditional>
344 <param name="overwrite_existing_file" value="Yes" />
345 <param name="add_metadata_column_to_object" value="Yes" />
346 <param name="represent_nan" value="NaN" />
347 <conditional name="con_measurement_export">
348 <param name="export_measurement" value="No" />
349 </conditional>
350 <param name="calc_mean" value="Yes" />
351 <param name="calc_median" value="Yes" />
352 <param name="calc_standard_deviation" value="Yes" />
353 <conditional name="con_create_gene_pattern">
354 <param name="create_gene_pattern" value="Yes" />
355 <conditional name="con_source_sample_row">
356 <param name="select_source_sample_row_name" value="Image filename" />
357 <param name="image_filename_cat" value="DNA" />
358 </conditional>
359 </conditional>
360 <conditional name="con_export_all_measurements">
361 <param name="export_all_measurements" value="No" />
362 <repeat name="r_data_to_export">
363 <param name="data_to_export" value="Image" />
364 <conditional name="con_obj_name_for_filename">
365 <param name="use_as_filename" value="No" />
366 <param name="file_name" value="data.csv" />
367 </conditional>
368 </repeat>
369 <repeat name="r_data_to_export">
370 <param name="data_to_export" value="Experiment" />
371 <conditional name="con_obj_name_for_filename">
372 <param name="use_as_filename" value="Yes" />
373 </conditional>
374 </repeat>
375 </conditional>
376 <expand macro="test_out_file" file="export_to_spreadsheet_multi.cppipe" />
225 </test> 377 </test>
226 </tests> 378 </tests>
227 379
228 <expand macro="help" module="ExportToSpreadsheet" /> 380 <help>
381 <![CDATA[
382 .. class:: infomark
383
384 **What it does**
385
386 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.
387
388 @COMMON_HELP@
389 ]]>
390 </help>
391
229 <expand macro="citations" /> 392 <expand macro="citations" />
230 393
231 </tool> 394 </tool>