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comparison MS2snoop.xml @ 6:77abacd33c31 draft

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planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
author workflow4metabolomics
date Fri, 30 Sep 2022 16:18:56 +0000
parents 78d5a12406c2
children 2a1f120a6874
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5:78d5a12406c2 6:77abacd33c31
1 <tool 1 <tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 id="ms2snoop"
3 name="MS2 Snoop"
4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
5 profile="21.09"
6 >
7 <description> 2 <description>
8 MS1/MS2 spectra and associated adducts extraction and cleaning 3 MS1/MS2 spectra and associated adducts extraction and cleaning
9 </description> 4 </description>
10 <macros> 5 <macros>
11 <import>macros.xml</import> 6 <import>macros.xml</import>
31 <exit_code range="4:254" level="fatal" description="Unknown error" /> 26 <exit_code range="4:254" level="fatal" description="Unknown error" />
32 <exit_code range="255" level="fatal" description="No any result to output" /> 27 <exit_code range="255" level="fatal" description="No any result to output" />
33 <regex match="Error in\s+.*:\s+.*" /> 28 <regex match="Error in\s+.*:\s+.*" />
34 </stdio> 29 </stdio>
35 <version_command> 30 <version_command>
36 Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1 31 <![CDATA[
32 @COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' --version | head -n 1
33 ]]>
37 </version_command> 34 </version_command>
38 <command> 35 <command>
39 <![CDATA[ 36 <![CDATA[
40 Rscript '$__tool_directory__/MS2snoop.R' 37 @COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R'
41 --output '$frag_result_txt' 38 --output '$frag_result_txt'
42 --compounds '$compound_txt' 39 --compounds '$compound_txt'
43 --fragments '$peaklist_frag_tsv' 40 --fragments '$peaklist_frag_tsv'
44 --precursors '$peaklist_preco_tsv' 41 --precursors '$peaklist_preco_tsv'
45 --tolmz '$tolmz' 42 --tolmz '$tolmz'
52 --fragment_match_delta '$sirius.fragment_match_delta' 49 --fragment_match_delta '$sirius.fragment_match_delta'
53 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit' 50 --fragment_match_delta_unit '$sirius.fragment_match_delta_unit'
54 $advenced.pdf 51 $advenced.pdf
55 $advenced.debug 52 $advenced.debug
56 $advenced.verbose 53 $advenced.verbose
57 ]]> 54 ]]>
58 </command> 55 </command>
59 <inputs> 56 <inputs>
60 <param 57 <param argument="--compound_txt" type="data" format="tabular,csv,tsv"
61 argument="--compound_txt"
62 type="data"
63 format="tabular,csv,tsv"
64 label="list of compounds" 58 label="list of compounds"
65 help=" 59 help="The table must fit the format: compound_name, inchikey, [elemcomposition], mz, rtsec."
66 The table must fit the format: 60 />
67 compound_name [MANDATORY] ; 61 <param argument="--peaklist_frag_tsv" type="data" format="tabular,csv,tsv"
68 inchikey [MANDATORY] ;
69 elemcomposition [OPTIONAL] ;
70 mz [MANDATORY] ;
71 rtsec [MANDATORY].
72 "
73 />
74 <param
75 argument="--peaklist_frag_tsv"
76 type="data"
77 format="tabular,csv,tsv"
78 label="MSpurity fragments file" 62 label="MSpurity fragments file"
79 /> 63 />
80 <param 64 <param argument="--peaklist_preco_tsv" type="data" format="tabular,csv,tsv"
81 argument="--peaklist_preco_tsv"
82 type="data"
83 format="tabular,csv,tsv"
84 label="MSpurity precursors file" 65 label="MSpurity precursors file"
85 /> 66 />
86 <param 67 <param argument="--tolmz" type="float" min="0.0001" max="10" value="0.01"
87 argument="--tolmz"
88 type="float"
89 min="0.0001"
90 max="10"
91 value="0.01"
92 label="MZ Tolerence" 68 label="MZ Tolerence"
93 help="M/z tolerance to determine if a precursor matches a compound" 69 help="M/z tolerance to determine if a precursor matches a compound"
94 /> 70 />
95 <param 71 <param argument="--tolrt" type="integer" min="0" max="30" value="20"
96 argument="--tolrt"
97 type="integer"
98 min="0"
99 max="30"
100 value="20"
101 label="RT Tolerence (in seconds)" 72 label="RT Tolerence (in seconds)"
102 help=" 73 help="Retention time tolerance to determine if a precursor matches a compound"
103 Retention time tolerance to determine if a 74 />
104 precursor matches a compound 75 <param argument="--seuil_ra" type="float" min="0" max="1" value="0.05"
105 "
106 />
107 <param
108 argument="--seuil_ra"
109 type="float"
110 min="0"
111 max="1"
112 value="0.05"
113 label="R-Pearson correlation threshold used to filter fragments" 76 label="R-Pearson correlation threshold used to filter fragments"
114 /> 77 />
115 <param 78 <param argument="--mzdecimal" type="integer" min="0" max="5" value="3"
116 argument="--mzdecimal"
117 type="integer"
118 min="0"
119 max="5"
120 value="0"
121 label="Number of decimal to output M/z values with" 79 label="Number of decimal to output M/z values with"
122 /> 80 />
123 <param 81 <param argument="--r_threshold" type="float" min="0" value="0.85"
124 argument="--r_threshold"
125 type="float"
126 min="0"
127 value="0.85"
128 label=" 82 label="
129 Minimun correlation with absolute intensity value to reach 83 Minimun correlation with absolute intensity value to reach
130 for a fragment to be considered as valid. 84 for a fragment to be considered as valid.
131 In PDF generation, invalid fragments will be 85 In PDF generation, invalid fragments will be
132 displayed in grey. 86 displayed in grey.
133 " 87 "
134 /> 88 />
135 <param 89 <param argument="--min_number_scan" type="integer" min="0" max="25" value="8"
136 argument="--min_number_scan"
137 type="integer"
138 min="0"
139 max="25"
140 value="8"
141 label="Present in at least X scan" 90 label="Present in at least X scan"
142 help=" 91 help="Mininum scan number in which a fragment must be found, to be kept."
143 Mininum scan number in which a fragment must be found,
144 to be kept.
145 "
146 /> 92 />
147 93
148 <section title="Sirius Parameters" name="sirius"> 94 <section title="Sirius Parameters" name="sirius">
149 <param 95 <param argument="--ionization" type="select" optional="true"
150 argument="--ionization"
151 type="select"
152 label="Which ionization" 96 label="Which ionization"
153 help="Select the ionization to use in sirius" 97 help="Select the ionization to use in sirius"
154 optional="true"
155 > 98 >
156 <option value="[M+H]+" selected="true">[M+H]+</option> 99 <option value="[M+H]+" selected="true">[M+H]+</option>
157 <option value="[M-H]-">[M-H]-</option> 100 <option value="[M-H]-">[M-H]-</option>
158 <option value="[M+?]+">[M+?]+</option> 101 <option value="[M+?]+">[M+?]+</option>
159 <option value="[M+K]+">[M+K]+</option> 102 <option value="[M+K]+">[M+K]+</option>
164 <option value="[M+Cl]-">[M+Cl]-</option> 107 <option value="[M+Cl]-">[M+Cl]-</option>
165 <option value="[M-H2O-H]-">[M-H2O-H]-</option> 108 <option value="[M-H2O-H]-">[M-H2O-H]-</option>
166 <option value="[M+Br]-">[M+Br]-</option> 109 <option value="[M+Br]-">[M+Br]-</option>
167 </param> 110 </param>
168 111
169 <param 112 <param argument="--fragment_match_delta" type="float" min="0" max="25" value="10"
170 argument="--fragment_match_delta"
171 type="float"
172 min="0"
173 max="25"
174 value="10"
175 label="Fragment match delta" 113 label="Fragment match delta"
176 help=" 114 help="
177 Delta that determines if a fragment found by sirius 115 Delta that determines if a fragment found by sirius
178 is linked to a certain M/z value. 116 is linked to a certain M/z value.
179 Zero means all fragments found by sirius will be 117 Zero means all fragments found by sirius will be
180 associated even when M/z difference is aberant. 118 associated even when M/z difference is aberant.
181 " 119 "
182 /> 120 />
183 <param 121 <param argument="--fragment_match_delta_unit" type="select" optional="true"
184 argument="--fragment_match_delta_unit"
185 type="select"
186 label="Delta unit" 122 label="Delta unit"
187 help="Select the unit of the fragment match delta" 123 help="Select the unit of the fragment match delta"
188 optional="true"
189 > 124 >
190 <option value="ppm" selected="true">PPM</option> 125 <option value="ppm" selected="true">PPM</option>
191 <option value="mz">M/z</option> 126 <option value="mz">M/z</option>
192 </param> 127 </param>
193 </section> 128 </section>
194 129
195 <section title="Advenced Options" name="advenced"> 130 <section title="Advenced Options" name="advenced">
196 <param 131 <param argument="--pdf" type="boolean" truevalue="--pdf_path '$pdf_output'" falsevalue="" value="" optional="true"
197 argument="--pdf"
198 type="boolean"
199 value=""
200 optional="true"
201 label="Output PDF" 132 label="Output PDF"
202 help="The tool will output some pdf in a zip file" 133 help="The tool will output some pdf in a zip file"
203 truevalue="--pdf_path '$pdf_output'"
204 falsevalue=""
205 /> 134 />
206 <param 135 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" value="" optional="true"
207 argument="--verbose"
208 type="boolean"
209 value=""
210 optional="true"
211 label="Verbose logs" 136 label="Verbose logs"
212 help="The tool will print more logs" 137 help="The tool will print more logs"
213 truevalue="--verbose"
214 falsevalue=""
215 /> 138 />
216 <param 139 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" value="" optional="true"
217 argument="--debug"
218 type="boolean"
219 value=""
220 optional="true"
221 label="Debug statements" 140 label="Debug statements"
222 help="The tool will print debug statements" 141 help="The tool will print debug statements"
223 truevalue="--debug"
224 falsevalue=""
225 /> 142 />
226 </section> 143 </section>
227 </inputs> 144 </inputs>
228 <outputs> 145 <outputs>
229 <data 146 <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" />
230 name="frag_result_txt" 147 <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}">
231 format="tsv"
232 label="${tool.name} on ${peaklist_frag_tsv.name}"
233 />
234 <data
235 name="pdf_output"
236 format="zip"
237 label="${tool.name} PDFs for ${peaklist_frag_tsv.name}"
238 >
239 <filter>advenced['pdf']</filter> 148 <filter>advenced['pdf']</filter>
240 </data> 149 </data>
241 </outputs> 150 </outputs>
242 <tests> 151 <tests>
243 <test> 152 <test>
244 <!-- Regular test with no option --> 153 <!-- Regular test with no option -->
245 <param 154 <param name="compound_txt" value="compounds_pos.txt" />
246 name="compound_txt" 155 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
247 value="compounds_pos.txt" 156 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
248 /> 157 <output name="frag_result_txt" file="compound_fragments_result.txt" />
249 <param
250 name="peaklist_frag_tsv"
251 value="peaklist_fragments.tsv"
252 />
253 <param
254 name="peaklist_preco_tsv"
255 value="peaklist_precursors.tsv"
256 />
257 <output
258 name="frag_result_txt"
259 file="compound_fragments_result.txt"
260 />
261 <assert_stdout> 158 <assert_stdout>
262 <expand macro="has_regular_stdout"/> 159 <expand macro="has_regular_stdout"/>
263 <expand macro="has_not_verbose_stdout"/> 160 <expand macro="has_not_verbose_stdout"/>
264 <expand macro="has_not_debug_stdout"/> 161 <expand macro="has_not_debug_stdout"/>
265 </assert_stdout> 162 </assert_stdout>
266 </test> 163 </test>
267 164
268 <test> 165 <test>
269 <!-- Regular files with verbose output --> 166 <!-- Regular files with verbose output -->
270 <param 167 <param name="compound_txt" value="compounds_pos.txt" />
271 name="compound_txt" 168 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
272 value="compounds_pos.txt" 169 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
273 />
274 <param
275 name="peaklist_frag_tsv"
276 value="peaklist_fragments.tsv"
277 />
278 <param
279 name="peaklist_preco_tsv"
280 value="peaklist_precursors.tsv"
281 />
282 <param name="verbose" value="--verbose" /> 170 <param name="verbose" value="--verbose" />
283 <output 171 <output name="frag_result_txt" file="compound_fragments_result.txt" />
284 name="frag_result_txt"
285 file="compound_fragments_result.txt"
286 />
287 <assert_stdout> 172 <assert_stdout>
288 <expand macro="has_regular_stdout"/> 173 <expand macro="has_regular_stdout"/>
289 <expand macro="has_verbose_stdout"/> 174 <expand macro="has_verbose_stdout"/>
290 <expand macro="has_not_debug_stdout"/> 175 <expand macro="has_not_debug_stdout"/>
291 </assert_stdout> 176 </assert_stdout>
292 </test> 177 </test>
293 178
294 <test> 179 <test>
295 <!-- Regular test with debug outputs --> 180 <!-- Regular test with debug outputs -->
296 <param 181 <param name="compound_txt" value="compounds_pos.txt" />
297 name="compound_txt" 182 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
298 value="compounds_pos.txt" 183 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
299 />
300 <param
301 name="peaklist_frag_tsv"
302 value="peaklist_fragments.tsv"
303 />
304 <param
305 name="peaklist_preco_tsv"
306 value="peaklist_precursors.tsv"
307 />
308 <param name="debug" value="--debug" /> 184 <param name="debug" value="--debug" />
309 <output 185 <output name="frag_result_txt" file="compound_fragments_result.txt" />
310 name="frag_result_txt"
311 file="compound_fragments_result.txt"
312 />
313 <assert_stdout> 186 <assert_stdout>
314 <expand macro="has_smol_stdout"/> 187 <expand macro="has_smol_stdout"/>
315 <expand macro="has_debug_stdout"/> 188 <expand macro="has_debug_stdout"/>
316 <expand macro="has_not_verbose_stdout"/> 189 <expand macro="has_not_verbose_stdout"/>
317 </assert_stdout> 190 </assert_stdout>
318 </test> 191 </test>
319 192
320 <test> 193 <test>
321 <!-- Regular test with both verbose and debug outputs --> 194 <!-- Regular test with both verbose and debug outputs -->
322 <param 195 <param name="compound_txt" value="compounds_pos.txt" />
323 name="compound_txt" 196 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
324 value="compounds_pos.txt" 197 <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" />
325 />
326 <param
327 name="peaklist_frag_tsv"
328 value="peaklist_fragments.tsv"
329 />
330 <param
331 name="peaklist_preco_tsv"
332 value="peaklist_precursors.tsv"
333 />
334 <param name="debug" value="--debug" /> 198 <param name="debug" value="--debug" />
335 <param name="verbose" value="--verbose" /> 199 <param name="verbose" value="--verbose" />
336 <output 200 <output name="frag_result_txt" file="compound_fragments_result.txt" />
337 name="frag_result_txt"
338 file="compound_fragments_result.txt"
339 />
340 <assert_stdout> 201 <assert_stdout>
341 <expand macro="has_smol_stdout"/> 202 <expand macro="has_smol_stdout"/>
342 <expand macro="has_debug_stdout"/> 203 <expand macro="has_debug_stdout"/>
343 <expand macro="has_smol_verbose_stdout"/> 204 <expand macro="has_smol_verbose_stdout"/>
344 </assert_stdout> 205 </assert_stdout>
347 <test> 208 <test>
348 <!-- 209 <!--
349 This test mixes tsv, csv, and so, and ms2snoop is expected 210 This test mixes tsv, csv, and so, and ms2snoop is expected
350 handle them like usual. 211 handle them like usual.
351 --> 212 -->
352 <param 213 <param name="compound_txt" value="compounds_pos.csv" />
353 name="compound_txt" 214 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
354 value="compounds_pos.csv" 215 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
355 />
356 <param
357 name="peaklist_frag_tsv"
358 value="peaklist_fragments.tsv"
359 />
360 <param
361 name="peaklist_preco_tsv"
362 value="peaklist_precursors.csv"
363 />
364 <param name="verbose" value="--verbose" /> 216 <param name="verbose" value="--verbose" />
365 <output 217 <output name="frag_result_txt" file="compound_fragments_result.txt" />
366 name="frag_result_txt"
367 file="compound_fragments_result.txt"
368 />
369 <assert_stdout> 218 <assert_stdout>
370 <expand macro="has_regular_stdout"/> 219 <expand macro="has_regular_stdout"/>
371 <expand macro="has_verbose_stdout"/> 220 <expand macro="has_verbose_stdout"/>
372 <expand macro="has_not_debug_stdout"/> 221 <expand macro="has_not_debug_stdout"/>
373 </assert_stdout> 222 </assert_stdout>
430 <test expect_exit_code="2" expect_failure="true"> 279 <test expect_exit_code="2" expect_failure="true">
431 <!-- 280 <!--
432 This test uses old format for molecules file. 281 This test uses old format for molecules file.
433 Is is expected to fail 282 Is is expected to fail
434 --> 283 -->
435 <param 284 <param name="compound_txt" value="compounds_pos_old_format.txt" />
436 name="compound_txt" 285 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
437 value="compounds_pos_old_format.txt" 286 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
438 />
439 <param
440 name="peaklist_frag_tsv"
441 value="peaklist_fragments.tsv"
442 />
443 <param
444 name="peaklist_preco_tsv"
445 value="peaklist_precursors.csv"
446 />
447 <assert_stderr> 287 <assert_stderr>
448 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" /> 288 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" />
449 </assert_stderr> 289 </assert_stderr>
450 </test> 290 </test>
451 291
452 </tests> 292 </tests>
453 <help><![CDATA[ 293 <help>
454 294 <![CDATA[
455 @AUTHORS@ 295 @AUTHORS@
456 296
457 ============== 297 ==============
458 MS2 validation 298 MS2 validation
459 ============== 299 ==============
506 | Input compounds file to search in precursor | | 346 | Input compounds file to search in precursor | |
507 +----------------------------------------------+------------+ 347 +----------------------------------------------+------------+
508 | and fragment (Name + m/z + ret Time) | TSV,CSV | 348 | and fragment (Name + m/z + ret Time) | TSV,CSV |
509 +----------------------------------------------+------------+ 349 +----------------------------------------------+------------+
510 350
511
512 @PARAMETERS@ 351 @PARAMETERS@
513
514
515 @OUTPUTS@ 352 @OUTPUTS@
516
517
518 @CHANGELOG@ 353 @CHANGELOG@
519 354 ]]>
520 ]]></help> 355 </help>
521 </tool> 356 </tool>