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comparison ramclustr.xml @ 8:c043e1fd79d1 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d
author recetox
date Tue, 16 Apr 2024 11:30:05 +0000
parents 09cabbc3d12d
children d70dd1d6ac4d
comparison
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7:09cabbc3d12d 8:c043e1fd79d1
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy3" profile="21.09"> 1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09">
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'/>
151 </conditional> 151 </conditional>
152 <expand macro="main_parameters" /> 152 <expand macro="main_parameters" />
153 </inputs> 153 </inputs>
154 154
155 <outputs> 155 <outputs>
156 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" /> 156 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" />
157 <expand macro="output_msp"/> 157 <expand macro="output_msp"/>
158 </outputs> 158 </outputs>
159 159
160 <tests> 160 <tests>
161 <test expect_num_outputs="2"><!-- TEST 1 --> 161 <test expect_num_outputs="2"><!-- TEST 1 -->
173 </section> 173 </section>
174 <section name="extras"> 174 <section name="extras">
175 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> 175 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
176 </section> 176 </section>
177 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/> 177 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
178 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> 178 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/>
179 </test> 179 </test>
180 <test expect_num_outputs="2"><!-- TEST 2 --> 180 <test expect_num_outputs="2"><!-- TEST 2 -->
181 <section name="filetype"> 181 <section name="filetype">
182 <param name="type_choice" value="xcms"/> 182 <param name="type_choice" value="xcms"/>
183 <section name="xcms"> 183 <section name="xcms">
194 <section name="normalisation_method"> 194 <section name="normalisation_method">
195 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> 195 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
196 </section> 196 </section>
197 </section> 197 </section>
198 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/> 198 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
199 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> 199 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/>
200 </test> 200 </test>
201 <test expect_num_outputs="2"><!-- TEST 3 --> 201 <test expect_num_outputs="2"><!-- TEST 3 -->
202 <section name="filetype"> 202 <section name="filetype">
203 <param name="type_choice" value="csv"/> 203 <param name="type_choice" value="csv"/>
204 <section name="ms_csv"> 204 <section name="ms_csv">
212 <section name="performance"> 212 <section name="performance">
213 <param name="blocksize" value="1000"/> 213 <param name="blocksize" value="1000"/>
214 <param name="mult" value="1"/> 214 <param name="mult" value="1"/>
215 </section> 215 </section>
216 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/> 216 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
217 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/> 217 <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/>
218 </test> 218 </test>
219 <test expect_num_outputs="2"><!-- TEST 4 --> 219 <test expect_num_outputs="2"><!-- TEST 4 -->
220 <section name="filetype"> 220 <section name="filetype">
221 <param name="type_choice" value="csv"/> 221 <param name="type_choice" value="csv"/>
222 <section name="ms_csv"> 222 <section name="ms_csv">