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comparison ramclustr.xml @ 12:f52181a205d3 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c562be4e9eb71470b480752aafe16722aee72bb1
author recetox
date Thu, 19 Jun 2025 07:59:00 +0000
parents da7722f665f4
children
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11:da7722f665f4 12:f52181a205d3
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy7" profile="21.09"> 1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0" profile="23.0">
2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description> 2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='annotation'/> 6 <expand macro='annotation'/>
13 <expand macro="refs"/> 13 <expand macro="refs"/>
14 <expand macro="creator"/> 14 <expand macro="creator"/>
15 15
16 <requirements> 16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
18 <requirement type="package" version="3.20.0">bioconductor-xcms</requirement> 18 <requirement type="package" version="3.22.0">bioconductor-xcms</requirement>
19 <requirement type="package" version="9.0.0">r-arrow</requirement> 19 <requirement type="package" version="19.0.1">r-arrow</requirement>
20 </requirements> 20 </requirements>
21 21
22 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="aggressive"><![CDATA[
23 Rscript 23 Rscript
24 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' 24 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
25 -e 'source("${ramclustr_method}")' 25 -e 'source("${ramclustr_method}")'
26 ]]> 26 ]]>
27 </command> 27 </command>
28 <configfiles> 28 <configfiles>
29 <configfile name="ramclustr_method"> 29 <configfile name="ramclustr_method">
30 #if $filetype.type_choice == "xcms": 30 #if $filetype.type_choice == "xcms":
31 obj = load("$filetype.xcms.input_xcms") 31 obj = load("$filetype.input_xcms")
32 ramclustObj = RAMClustR::rc.get.xcms.data( 32 ramclustObj = RAMClustR::rc.get.xcms.data(
33 xcmsObj = xdata, 33 xcmsObj = xdata,
34 #if $extras.ExpDes: 34 #if $extras.ExpDes:
35 ExpDes = load_experiment_definition("${$extras.ExpDes}"), 35 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
36 #end if 36 #end if
120 hmax = $clustering.hmax, 120 hmax = $clustering.hmax,
121 minModuleSize = $clustering.minModuleSize, 121 minModuleSize = $clustering.minModuleSize,
122 linkage = "$clustering.linkage", 122 linkage = "$clustering.linkage",
123 cor.method = "$filetype.required.cor_method", 123 cor.method = "$filetype.required.cor_method",
124 rt.only.low.n = $extras.rt_only_low_n, 124 rt.only.low.n = $extras.rt_only_low_n,
125 fftempdir = NULL,
126 ) 125 )
127 126
128 #if $extras.quality_control == "TRUE": 127 #if $extras.quality_control == "TRUE":
129 ramclustObj = RAMClustR::rc.qc(ramclustObj = ramclustObj) 128 ramclustObj = RAMClustR::rc.qc(ramclustObj = ramclustObj)
130 #end if 129 #end if
175 </conditional> 174 </conditional>
176 <expand macro="main_parameters" /> 175 <expand macro="main_parameters" />
177 </inputs> 176 </inputs>
178 177
179 <outputs> 178 <outputs>
180 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" /> 179 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tabular" />
181 <expand macro="output_msp"/> 180 <expand macro="output_msp"/>
182 </outputs> 181 </outputs>
183 182
184 <tests> 183 <tests>
185 <test expect_num_outputs="2"><!-- TEST 1 --> 184 <!-- TEST 1 -->
186 <section name="filetype"> 185 <test expect_num_outputs="2">
186 <conditional name="filetype">
187 <param name="type_choice" value="xcms"/> 187 <param name="type_choice" value="xcms"/>
188 <section name="xcms"> 188 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
189 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
190 </section>
191 <section name="required"> 189 <section name="required">
192 <param name="maxt" value="259.8"/> 190 <param name="maxt" value="259.8"/>
193 </section> 191 </section>
194 </section> 192 </conditional>
195 <section name="msp_output_details"> 193 <section name="msp_output_details">
196 <param name="mzdec" value="4"/> 194 <param name="mzdec" value="4"/>
197 </section> 195 </section>
198 <section name="extras"> 196 <section name="extras">
199 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> 197 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
200 </section> 198 </section>
201 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/> 199 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
202 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/> 200 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tabular" compare="sim_size" delta="100"/>
203 </test> 201 </test>
204 <test expect_num_outputs="2"><!-- TEST 2 --> 202
205 <section name="filetype"> 203 <!-- TEST 2 -->
204 <test expect_num_outputs="2">
205 <conditional name="filetype">
206 <param name="type_choice" value="xcms"/> 206 <param name="type_choice" value="xcms"/>
207 <section name="xcms"> 207 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
208 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
209 </section>
210 <section name="required"> 208 <section name="required">
211 <param name="maxt" value="78.4"/> 209 <param name="maxt" value="78.4"/>
212 </section> 210 </section>
213 </section> 211 </conditional>
214 <section name="msp_output_details"> 212 <section name="msp_output_details">
215 <param name="mzdec" value="4"/> 213 <param name="mzdec" value="4"/>
216 </section> 214 </section>
217 <section name="normalisation"> 215 <section name="normalisation">
218 <section name="normalisation_method"> 216 <conditional name="normalisation_method">
219 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> 217 <param name="normalize" value="quantile"/>
220 </section> 218 </conditional>
221 </section> 219 </section>
222 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/> 220 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="500"/>
223 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/> 221 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tabular" compare="sim_size" delta="500"/>
224 </test> 222 </test>
225 <test expect_num_outputs="2"><!-- TEST 3 --> 223
226 <section name="filetype"> 224 <!-- TEST 3 -->
225 <test expect_num_outputs="2">
226 <conditional name="filetype">
227 <param name="type_choice" value="csv"/> 227 <param name="type_choice" value="csv"/>
228 <section name="ms_csv"> 228 <section name="ms_csv">
229 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> 229 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
230 </section> 230 </section>
231 <section name="required"> 231 <section name="required">
232 <param name="st" value="5.0"/> 232 <param name="st" value="5.0"/>
233 <param name="maxt" value="1"/> 233 <param name="maxt" value="1"/>
234 </section> 234 </section>
235 </section> 235 </conditional>
236 <section name="performance"> 236 <section name="performance">
237 <param name="blocksize" value="1000"/> 237 <param name="blocksize" value="1000"/>
238 <param name="mult" value="1"/> 238 <param name="mult" value="1"/>
239 </section> 239 </section>
240 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/> 240 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
241 <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/> 241 <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tabular"/>
242 </test> 242 </test>
243 <test expect_num_outputs="2"><!-- TEST 4 --> 243
244 <section name="filetype"> 244 <!-- TEST 4 -->
245 <test expect_num_outputs="2">
246 <conditional name="filetype">
245 <param name="type_choice" value="csv"/> 247 <param name="type_choice" value="csv"/>
246 <section name="ms_csv"> 248 <section name="ms_csv">
247 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> 249 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
248 </section> 250 </section>
249 </section> 251 </conditional>
250 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/> 252 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
251 </test> 253 </test>
252 <test expect_num_outputs="2"><!-- TEST 5 --> 254
253 <section name="filetype"> 255 <!-- TEST 5 -->
256 <test expect_num_outputs="2">
257 <conditional name="filetype">
254 <param name="type_choice" value="recetox-aplcms"/> 258 <param name="type_choice" value="recetox-aplcms"/>
255 <section name="ms_dataframe"> 259 <section name="ms_dataframe">
256 <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/> 260 <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/>
257 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/> 261 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
258 </section> 262 </section>
259 </section> 263 </conditional>
260 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/> 264 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
261 </test> 265 </test>
262 <test expect_num_outputs="3"><!-- TEST 6 --> 266
263 <section name="filetype"> 267 <!-- TEST 6 -->
268 <test expect_num_outputs="3">
269 <conditional name="filetype">
264 <param name="type_choice" value="xcms"/> 270 <param name="type_choice" value="xcms"/>
265 <section name="xcms"> 271 <param name="input_xcms" value="test6.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
266 <param name="input_xcms" value="test6.fillpeaks" ftype="rdata.xcms.fillpeaks"/> 272 </conditional>
267 </section>
268 </section>
269 <section name="msp_output_details"> 273 <section name="msp_output_details">
270 <param name="mzdec" value="4"/> 274 <param name="mzdec" value="4"/>
271 </section> 275 </section>
272 <section name="extras"> 276 <section name="extras">
273 <param name="quality_control" value="TRUE"/> 277 <param name="quality_control" value="TRUE"/>
274 </section> 278 </section>
275 <section name="filtering"> 279 <section name="filtering">
276 <section name="feature_filter_blanks"> 280 <conditional name="feature_filter_blanks">
277 <param name="filter_blanks" value="TRUE"/> 281 <param name="filter_blanks" value="TRUE"/>
278 <param name="blank_tag" value="Blanc"/> 282 <param name="blank_tag" value="Blanc"/>
279 </section> 283 </conditional>
280 <section name="feature_filter_cv"> 284 <conditional name="feature_filter_cv">
281 <param name="filter_cv" value="TRUE"/> 285 <param name="filter_cv" value="TRUE"/>
282 </section> 286 </conditional>
283 </section> 287 </section>
284 <output name="mass_spectra_merged" file="test6_out.msp" ftype="msp"/> 288 <output name="mass_spectra_merged" file="test6_out.msp" ftype="msp"/>
285 <output name="spec_abundance"> 289 <output name="spec_abundance">
286 <assert_contents> 290 <assert_contents>
287 <has_size value="309" delta="10"/> 291 <has_size value="309" delta="10"/>