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comparison common.xml @ 1:0b7db679fff8 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6a3036d24b5ec074936f8f8283b7e176f6f1ce70"
author bgruening
date Thu, 09 Apr 2020 08:12:15 -0400
parents 9c8ee01c0b22
children
comparison
equal deleted inserted replaced
0:9c8ee01c0b22 1:0b7db679fff8
180 _str += FOURSPACES + "Assignments count:%s\n" % rule_count 180 _str += FOURSPACES + "Assignments count:%s\n" % rule_count
181 _str += FOURSPACES + "Single images count:0\n" 181 _str += FOURSPACES + "Single images count:0\n"
182 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity 182 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
183 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d 183 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
184 184
185 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" + x_spacing 185 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
186 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" + y_spacing 186 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
187 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" + z_spacing 187 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
188 else: 188 else:
189 _str += FOURSPACES + "Select the image type:Grayscale image\n" 189 _str += FOURSPACES + "Select the image type:Grayscale image\n"
190 _str += FOURSPACES + "Name to assign these images:DNA\n" 190 _str += FOURSPACES + "Name to assign these images:DNA\n"
191 _str += FOURSPACES + "Match metadata:[]\n" 191 _str += FOURSPACES + "Match metadata:[]\n"
192 192
216 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"] 216 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
217 else: 217 else:
218 _str += FOURSPACES + "Maximum intensity:255.0\n" 218 _str += FOURSPACES + "Maximum intensity:255.0\n"
219 219
220 if process_3d == "Yes": 220 if process_3d == "Yes":
221 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" + x_spacing 221 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
222 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" + y_spacing 222 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
223 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" + z_spacing 223 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
224 224
225 return _str 225 return _str
226 226
227 227
228 def write_groups(): 228 def write_groups():
303 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option> 303 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
304 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option> 304 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
305 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option> 305 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
306 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option> 306 <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
307 </param> 307 </param>
308 <param name="folder_name_regex" type="text" value="(?P&lt;Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$" label="Regular expression to extract from folder name"> 308 <param name="folder_name_regex" type="select" label="Select folder name pattern to extract from folder name" help="Folder names must comply with one of the patterns.For example, folder name images-exp1 matches the pattern field1-field2. If none of the patterns are suitable, please use other Galaxy tools to rename your folder first. ">
309 <sanitizer sanitize="false"/> 309 <sanitizer sanitize="false"/>
310 <option value="(?P&lt;field1>.*)">field1</option>
311 <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
312 <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
310 </param> 313 </param>
311 <param name="extract_metadata_from" type="select" label="Extract metadata from"> 314 <param name="extract_metadata_from" type="select" label="Extract metadata from">
312 <option value="All images">All images</option> 315 <option value="All images">All images</option>
313 <option value="Images matching a rule">Images matching a rule</option> 316 <option value="Images matching a rule">Images matching a rule</option>
314 </param> 317 </param>