Mercurial > repos > galaxyp > cardinal_single_ion_segmentation
comparison spatial_DGMM.xml @ 2:db423b7bce78 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author | galaxyp |
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date | Thu, 04 Jul 2024 13:43:40 +0000 |
parents | 4cb6c83d3777 |
children |
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1:53a2f4fa6cd2 | 2:db423b7bce78 |
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1 <tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0"> | 1 <tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> |
2 <description>mass spectrometry imaging spatial DGMM</description> | 2 <description>mass spectrometry imaging spatial DGMM</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"/> |
7 <requirement type="package" version="2.3">r-gridextra</requirement> | |
8 </expand> | |
9 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
10 <![CDATA[ | 8 <![CDATA[ |
11 | 9 |
12 @INPUT_LINKING@ | 10 @INPUT_LINKING@ |
13 cat '${MSI_spatial_DGMM}' && | 11 cat '${MSI_spatial_DGMM}' && |
64 if (npeaks > 0) | 62 if (npeaks > 0) |
65 { | 63 { |
66 | 64 |
67 ## set seed to make analysis reproducible | 65 ## set seed to make analysis reproducible |
68 set.seed($setseed) | 66 set.seed($setseed) |
69 | |
70 | 67 |
71 ## single ion segmentation | 68 ## single ion segmentation |
72 dgmm <- spatialDGMM(msidata, | 69 dgmm <- spatialDGMM(msidata, |
73 r = c($r), | 70 r = c($r), |
74 k = c($k), | 71 k = c($k), |
154 <when value="single_group"/> | 151 <when value="single_group"/> |
155 <when value="multiple_groups"> | 152 <when value="multiple_groups"> |
156 <expand macro="reading_pixel_annotations"/> | 153 <expand macro="reading_pixel_annotations"/> |
157 </when> | 154 </when> |
158 </conditional> | 155 </conditional> |
159 <param name="r" type="text" value="2" | 156 <param name="r" type="text" value="2" |
160 label="r" help="The spatial neighborhood radius of nearby pixels to consider. Only a single value is allowed"> | 157 label="r" help="The spatial neighborhood radius of nearby pixels to consider. Only a single value is allowed"> |
161 <expand macro="sanitizer_multiple_digits"/> | 158 <expand macro="sanitizer_multiple_digits"/> |
162 </param> | 159 </param> |
163 <param name="k" type="text" value="5" | 160 <param name="k" type="text" value="5" |
164 label="k" help="The maximum number of segments (clusters). The final number of segments may differ. Only a single value is allowed."> | 161 label="k" help="The maximum number of segments (clusters). The final number of segments may differ. Only a single value is allowed."> |
211 <filter>output_plots</filter> | 208 <filter>output_plots</filter> |
212 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_plots" format="tabular"/> | 209 <discover_datasets pattern="__designation_and_ext__" directory="DGMM_plots" format="tabular"/> |
213 </collection> | 210 </collection> |
214 </outputs> | 211 </outputs> |
215 <tests> | 212 <tests> |
216 <test> | 213 <test expect_num_outputs="4"> |
217 <param name="infile" value="" ftype="imzml"> | 214 <param name="infile" value="" ftype="imzml"> |
218 <composite_data value="spatial_DGMM_input.imzML"/> | 215 <composite_data value="spatial_DGMM_input.imzML"/> |
219 <composite_data value="spatial_DGMM_input.ibd"/> | 216 <composite_data value="spatial_DGMM_input.ibd"/> |
220 </param> | 217 </param> |
221 <param name="r" value="1"/> | 218 <param name="r" value="1"/> |
222 <param name="k" value="6"/> | 219 <param name="k" value="6"/> |
223 <param name="method" value="adaptive"/> | 220 <param name="method" value="adaptive"/> |
224 <param name="dist" value="radial"/> | 221 <param name="dist" value="radial"/> |
225 <param name="annealing" value="TRUE"/> | 222 <param name="annealing" value="TRUE"/> |
223 <param name="setseed" value="7353"/> | |
226 <param name="output_estimates" value="True"/> | 224 <param name="output_estimates" value="True"/> |
227 <param name="output_probability" value="True"/> | 225 <param name="output_probability" value="True"/> |
228 <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/> | 226 <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/> |
229 <output name="dgmm_summary" file="dgmm_summary1.tabular"/> | 227 <output name="dgmm_summary" file="dgmm_summary1.tabular"/> |
230 <output_collection name="estimates_output" type="list" count="10"> | 228 <output_collection name="estimates_output" type="list" count="10"> |
231 <element name="estimates_r1_k6_mz1135.93347167969" file="estimates_r1_k6_mz1135.93347167969.tabular"/> | 229 <element name="estimates_r1_k6_mz1135.93347167969"> |
230 <assert_contents> | |
231 <has_text text="files_"/> | |
232 <has_text text="3"/> | |
233 <has_text_matching expression="0\.\d+"/> | |
234 </assert_contents> | |
235 </element> | |
232 </output_collection> | 236 </output_collection> |
233 <output_collection name="probability_output" type="list" count="10"> | 237 <output_collection name="probability_output" type="list" count="10"> |
234 <element name="probability_r1_k6_mz1023.70806884766" file="probability_r1_k6_mz1023.70806884766.tabular"/> | 238 <element name="probability_r1_k6_mz1023.70806884766"> |
239 <assert_contents> | |
240 <has_text text="xy_16_1"/> | |
241 <has_text text="3"/> | |
242 <has_text_matching expression="0\.\d+"/> | |
243 </assert_contents> | |
244 </element> | |
235 </output_collection> | 245 </output_collection> |
236 </test> | 246 </test> |
237 <test> | 247 <test expect_num_outputs="6"> |
238 <param name="infile" value="" ftype="imzml"> | 248 <param name="infile" value="" ftype="imzml"> |
239 <composite_data value="spatial_DGMM_input.imzML"/> | 249 <composite_data value="spatial_DGMM_input.imzML"/> |
240 <composite_data value="spatial_DGMM_input.ibd"/> | 250 <composite_data value="spatial_DGMM_input.ibd"/> |
241 </param> | 251 </param> |
242 <conditional name="sample_groups"> | 252 <conditional name="sample_groups"> |
243 <param name="group" value="multiple_groups"/> | 253 <param name="group" value="multiple_groups"/> |
244 <param name="annotation_file" value="DGMM_annotations.tabular"/> | 254 <param name="annotation_file" value="DGMM_annotations.tabular"/> |
245 <param name="column_x" value="1"/> | 255 <param name="column_x" value="1"/> |
246 <param name="column_y" value="2"/> | 256 <param name="column_y" value="2"/> |
247 <param name="column_names" value="3"/> | 257 <param name="column_names" value="3"/> |
248 <param name="tabular_header" value="True"/> | 258 <param name="tabular_header" value="True"/> |
249 </conditional> | 259 </conditional> |
250 <param name="r" value="2"/> | 260 <param name="r" value="2"/> |
251 <param name="k" value="10"/> | 261 <param name="k" value="10"/> |
252 <param name="annealing" value="TRUE"/> | 262 <param name="annealing" value="TRUE"/> |
253 <param name="output_estimates" value="True"/> | 263 <param name="setseed" value="7353"/> |
254 <param name="output_probability" value="True"/> | 264 <param name="output_estimates" value="True"/> |
255 <param name="output_plots" value="True"/> | 265 <param name="output_probability" value="True"/> |
256 <param name="output_rdata" value="True"/> | 266 <param name="output_plots" value="True"/> |
257 <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/> | 267 <param name="output_rdata" value="True"/> |
258 <output name="dgmm_summary" file="dgmm_summary2.tabular"/> | 268 <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/> |
259 <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/> | 269 <output name="dgmm_summary" file="dgmm_summary2.tabular"/> |
260 <output_collection name="estimates_output" type="list" count="10"> | 270 <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/> |
261 <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/> | 271 <output_collection name="estimates_output" type="list" count="10"> |
262 </output_collection> | 272 <element name="estimates_r2_k10_mz1200.46533203125"> |
263 <output_collection name="probability_output" type="list" count="10"> | 273 <assert_contents> |
264 <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/> | 274 <has_text text="circle"/> |
265 </output_collection> | 275 <has_text text="3"/> |
276 <has_text_matching expression="0\.\d+"/> | |
277 </assert_contents> | |
278 </element> | |
279 </output_collection> | |
280 <output_collection name="probability_output" type="list" count="10"> | |
281 <element name="probability_r2_k10_mz1135.93347167969"> | |
282 <assert_contents> | |
283 <has_text text="xy_9_1"/> | |
284 <has_text text="3"/> | |
285 <has_text_matching expression="0\.\d+"/> | |
286 </assert_contents> | |
287 </element> | |
288 </output_collection> | |
266 </test> | 289 </test> |
267 </tests> | 290 </tests> |
268 <help> | 291 <help> |
269 <![CDATA[ | 292 <![CDATA[ |
270 | 293 |