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comparison spatial_DGMM.xml @ 2:db423b7bce78 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author galaxyp
date Thu, 04 Jul 2024 13:43:40 +0000
parents 4cb6c83d3777
children
comparison
equal deleted inserted replaced
1:53a2f4fa6cd2 2:db423b7bce78
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