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comparison MS2snoop.xml @ 4:856001213966 draft

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planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715
author workflow4metabolomics
date Wed, 06 Jul 2022 10:38:39 +0000
parents c68c94865667
children 78d5a12406c2
comparison
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3:c68c94865667 4:856001213966
2 <description> 2 <description>
3 MS1/MS2 spectra and associated adducts extraction and cleaning 3 MS1/MS2 spectra and associated adducts extraction and cleaning
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <token name="@TOOL_VERSION@">1.1.0</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 </macros> 7 </macros>
10 <edam_topics> 8 <edam_topics>
11 <edam_topic>topic_0091</edam_topic> 9 <edam_topic>topic_0091</edam_topic>
12 <edam_topic>topic_3370</edam_topic> 10 <edam_topic>topic_3370</edam_topic>
13 </edam_topics> 11 </edam_topics>
240 <expand macro="has_smol_stdout"/> 238 <expand macro="has_smol_stdout"/>
241 <expand macro="has_debug_stdout"/> 239 <expand macro="has_debug_stdout"/>
242 <expand macro="has_smol_verbose_stdout"/> 240 <expand macro="has_smol_verbose_stdout"/>
243 </assert_stdout> 241 </assert_stdout>
244 </test> 242 </test>
243 <test expect_exit_code="2" expect_failure="true">
244 <param name="compound_txt" value="compounds_pos_old_format.txt" />
245 <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" />
246 <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" />
247 <assert_stderr>
248 <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" />
249 </assert_stderr>
250 </test>
245 </tests> 251 </tests>
246 <help><![CDATA[ 252 <help><![CDATA[
247 .. class:: infomark 253
248 254 @AUTHORS@
249 **Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr)
250
251 .. class:: infomark
252
253 ---------------------------------------------------
254
255 255
256 ============== 256 ==============
257 MS2 validation 257 MS2 validation
258 ============== 258 ==============
259 259
260 ----------- 260 -----------
261 Description 261 Description
262 ----------- 262 -----------
263 263
264 MS2snoop use results of msPurity to find spectra of standards listed in a compounds file. 264 MS2snoop use results of msPurity to find spectra of standards listed in
265 Check the fragments and precursor using correlation of among the different scans of fragments 265 a compounds file. Check the fragments and precursor using correlation of
266 among the different scans of fragments
266 267
267 ----------------- 268 -----------------
268 Workflow position 269 Workflow position
269 ----------------- 270 -----------------
270 271
296 ----------- 297 -----------
297 298
298 +----------------------------------------------+------------+ 299 +----------------------------------------------+------------+
299 | Parameter : num + label | Format | 300 | Parameter : num + label | Format |
300 +===========================+==================+============+ 301 +===========================+==================+============+
301 | Input from msPurity Precursor | TSV | 302 | Input from msPurity Precursor | TSV,CSV |
302 +----------------------------------------------+------------+ 303 +----------------------------------------------+------------+
303 | Input from msPurity fragment | TSV | 304 | Input from msPurity fragment | TSV,CSV |
304 | Input compounds file to search in precursor | | 305 | Input compounds file to search in precursor | |
305 +----------------------------------------------+------------+ 306 +----------------------------------------------+------------+
306 | and fragment (Name + m/z + ret Time) | TSV | 307 | and fragment (Name + m/z + ret Time) | TSV,CSV |
307 +----------------------------------------------+------------+ 308 +----------------------------------------------+------------+
308 309
309 310
310 ---------- 311 @PARAMETERS@
311 Parameters 312
312 ---------- 313
313 314 @OUTPUTS@
314 msPurity.purityA 315
315 | output TSV file 316
316 317 @CHANGELOG@
317 msPurity.frag4feature 318
318 | output TSV file
319
320 Compounds file
321 | A TSV TXT file with a list of compounds with at least 3 columns :
322 | col1=Name of molecule, col2=m/z, col3=retention time
323
324 tolerance for mz(dalton) rt(seconds) to match the standard in the compounds file with the precursor MSpurity files
325 | tolmz <- 0.01
326 | tolrt <- 20
327
328 relative intensity threshold
329 | seuil_ra = 0.05
330
331 nb decimal for mz
332 | mzdecimal <- 0
333
334 r pearson correlation threshold between precursor and fragment absolute intensity
335 | r_threshold <- 0.85
336
337 fragments are kept if there are found in a minimum number of scans
338 | minNumberScan <- 8
339
340 ------------
341 Output files
342 ------------
343
344 compound_fragments_result.tsv
345 | tabular output
346 | Array with p rows (corresponding to the fragments for the different compounds of the compounds file)
347 | Last column "corvalid" is a boolean for validated fragments
348
349 processing_file.pdf
350 | pdf output
351 | For each compound of the compounds file, Graph of the all fragments with parents (or most intense peak if parent is not detected in the fragments. At the end the pdf file a graph of the spectra with validated fragments.
352 ]]></help> 319 ]]></help>
353 </tool> 320 </tool>