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comparison MS2snoop.xml @ 7:2a1f120a6874 draft default tip

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planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723
author workflow4metabolomics
date Tue, 10 Jan 2023 11:07:48 +0000
parents 77abacd33c31
children
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6:77abacd33c31 7:2a1f120a6874
46 --r_threshold '$r_threshold' 46 --r_threshold '$r_threshold'
47 --min_number_scan '$min_number_scan' 47 --min_number_scan '$min_number_scan'
48 --ionization '$sirius.ionization' 48 --ionization '$sirius.ionization'
49 --fragment_match_delta '$sirius.fragment_match_delta' 49 --fragment_match_delta '$sirius.fragment_match_delta'
50 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit' 50 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit'
51 $advenced.pdf 51 #if $advenced.pdf:
52 --pdf_path './out.zip'
53 #end if
52 $advenced.debug 54 $advenced.debug
53 $advenced.verbose 55 $advenced.verbose
56 #if $advenced.pdf:
57 && cat ./out.zip > '$pdf_output'
58 #end if
59
54 ]]> 60 ]]>
55 </command> 61 </command>
56 <inputs> 62 <inputs>
57 <param argument="--compound_txt" type="data" format="tabular,csv,tsv" 63 <param argument="--compound_txt" type="data" format="tabular,csv,tsv"
58 label="list of compounds" 64 label="list of compounds"
126 <option value="mz">M/z</option> 132 <option value="mz">M/z</option>
127 </param> 133 </param>
128 </section> 134 </section>
129 135
130 <section title="Advenced Options" name="advenced"> 136 <section title="Advenced Options" name="advenced">
131 <param argument="--pdf" type="boolean" truevalue="--pdf_path '$pdf_output'" falsevalue="" value="" optional="true" 137 <param argument="--pdf" type="boolean" value="" optional="true"
132 label="Output PDF" 138 label="Output PDF"
133 help="The tool will output some pdf in a zip file" 139 help="The tool will output some pdf in a zip file"
134 /> 140 />
135 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" value="" optional="true" 141 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" value="" optional="true"
136 label="Verbose logs" 142 label="Verbose logs"
141 help="The tool will print debug statements" 147 help="The tool will print debug statements"
142 /> 148 />
143 </section> 149 </section>
144 </inputs> 150 </inputs>
145 <outputs> 151 <outputs>
146 <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" /> 152 <data name="frag_result_txt" format="tsv" label="${tool.name}_on_${peaklist_frag_tsv.name}" />
147 <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}"> 153 <data name="pdf_output" format="zip" label="${tool.name}_PDFs_for_${peaklist_frag_tsv.name}">
148 <filter>advenced['pdf']</filter> 154 <filter>advenced['pdf']</filter>
149 </data> 155 </data>
150 </outputs> 156 </outputs>
151 <tests> 157 <tests>
152 <test> 158 <test>
153 <!-- Regular test with no option --> 159 <!-- #1 Regular test with no option -->
154 <param name="compound_txt" value="compounds_pos.txt" /> 160 <param name="compound_txt" value="compounds_pos.txt" />
155 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 161 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
156 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> 162 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
157 <output name="frag_result_txt" file="compound_fragments_result.txt" /> 163 <output name="frag_result_txt" file="compound_fragments_result.txt" />
158 <assert_stdout> 164 <assert_stdout>
161 <expand macro="has_not_debug_stdout"/> 167 <expand macro="has_not_debug_stdout"/>
162 </assert_stdout> 168 </assert_stdout>
163 </test> 169 </test>
164 170
165 <test> 171 <test>
166 <!-- Regular files with verbose output --> 172 <!-- #2 Regular files with verbose output -->
167 <param name="compound_txt" value="compounds_pos.txt" /> 173 <param name="compound_txt" value="compounds_pos.txt" />
168 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 174 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
169 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> 175 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
170 <param name="verbose" value="--verbose" /> 176 <param name="verbose" value="--verbose" />
171 <output name="frag_result_txt" file="compound_fragments_result.txt" /> 177 <output name="frag_result_txt" file="compound_fragments_result.txt" />
175 <expand macro="has_not_debug_stdout"/> 181 <expand macro="has_not_debug_stdout"/>
176 </assert_stdout> 182 </assert_stdout>
177 </test> 183 </test>
178 184
179 <test> 185 <test>
180 <!-- Regular test with debug outputs --> 186 <!-- #3 Regular test with debug outputs -->
181 <param name="compound_txt" value="compounds_pos.txt" /> 187 <param name="compound_txt" value="compounds_pos.txt" />
182 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 188 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
183 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> 189 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
184 <param name="debug" value="--debug" /> 190 <param name="debug" value="--debug" />
185 <output name="frag_result_txt" file="compound_fragments_result.txt" /> 191 <output name="frag_result_txt" file="compound_fragments_result.txt" />
189 <expand macro="has_not_verbose_stdout"/> 195 <expand macro="has_not_verbose_stdout"/>
190 </assert_stdout> 196 </assert_stdout>
191 </test> 197 </test>
192 198
193 <test> 199 <test>
194 <!-- Regular test with both verbose and debug outputs --> 200 <!-- #4 Regular test with both verbose and debug outputs -->
195 <param name="compound_txt" value="compounds_pos.txt" /> 201 <param name="compound_txt" value="compounds_pos.txt" />
196 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 202 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
197 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> 203 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
198 <param name="debug" value="--debug" /> 204 <param name="debug" value="--debug" />
199 <param name="verbose" value="--verbose" /> 205 <param name="verbose" value="--verbose" />
205 </assert_stdout> 211 </assert_stdout>
206 </test> 212 </test>
207 213
208 <test> 214 <test>
209 <!-- 215 <!--
210 This test mixes tsv, csv, and so, and ms2snoop is expected 216 #5 This test mixes tsv, csv, and so, and ms2snoop is expected
211 handle them like usual. 217 handle them like usual.
212 --> 218 -->
213 <param name="compound_txt" value="compounds_pos.csv" /> 219 <param name="compound_txt" value="compounds_pos.csv" />
214 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 220 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
215 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> 221 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
222 </assert_stdout> 228 </assert_stdout>
223 </test> 229 </test>
224 230
225 <test> 231 <test>
226 <!-- 232 <!--
227 This test contains smaller datasets. This is the "regular" 233 #6 This test contains smaller datasets. This is the "regular"
228 smol test, to prepare further smolah tests. 234 smol test, to prepare further smolah tests.
229 --> 235 -->
230 <param name="ionization" value="[M+?]+" /> 236 <param name="ionization" value="[M+?]+" />
231 <param name="mzdecimal" value="3" /> 237 <param name="mzdecimal" value="3" />
232 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> 238 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
235 <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> 241 <output name="frag_result_txt" file="smol/out-smol-base.tsv" />
236 </test> 242 </test>
237 243
238 <test> 244 <test>
239 <!-- 245 <!--
240 Test for pdf generation 246 #7 Test for pdf generation
241 --> 247 -->
242 <param name="pdf" value="True" /> 248 <param name="pdf" value="True" />
243 <param name="ionization" value="[M+?]+" /> 249 <param name="ionization" value="[M+?]+" />
244 <param name="mzdecimal" value="3" /> 250 <param name="mzdecimal" value="3" />
245 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> 251 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
248 <output name="frag_result_txt" file="smol/out-smol-base.tsv" /> 254 <output name="frag_result_txt" file="smol/out-smol-base.tsv" />
249 </test> 255 </test>
250 256
251 <test> 257 <test>
252 <!-- 258 <!--
253 test for delta in ppm 259 #8 test for delta in ppm
254 --> 260 -->
255 <param name="ionization" value="[M+?]+" /> 261 <param name="ionization" value="[M+?]+" />
256 <param name="mzdecimal" value="3" /> 262 <param name="mzdecimal" value="3" />
257 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> 263 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
258 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> 264 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" />
261 <output name="frag_result_txt" file="smol/out-smol-delta-8.542.tsv" /> 267 <output name="frag_result_txt" file="smol/out-smol-delta-8.542.tsv" />
262 </test> 268 </test>
263 269
264 <test> 270 <test>
265 <!-- 271 <!--
266 test for delta in m/z 272 #9 test for delta in m/z
267 --> 273 -->
268 <param name="ionization" value="[M+?]+" /> 274 <param name="ionization" value="[M+?]+" />
269 <param name="mzdecimal" value="3" /> 275 <param name="mzdecimal" value="3" />
270 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/> 276 <param name="compound_txt" value="smol/smol_compounds_pos.csv"/>
271 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" /> 277 <param name="peaklist_frag_tsv" value="smol/smol_fragments.tsv" />
276 </test> 282 </test>
277 283
278 <!-- === expected to fail tests === --> 284 <!-- === expected to fail tests === -->
279 <test expect_exit_code="2" expect_failure="true"> 285 <test expect_exit_code="2" expect_failure="true">
280 <!-- 286 <!--
281 This test uses old format for molecules file. 287 #10 This test uses old format for molecules file.
282 Is is expected to fail 288 Is is expected to fail
283 --> 289 -->
284 <param name="compound_txt" value="compounds_pos_old_format.txt" /> 290 <param name="compound_txt" value="compounds_pos_old_format.txt" />
285 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> 291 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
286 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> 292 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />