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comparison msconvert_win/msconvert_macros.xml @ 4:158a71ee5733 draft

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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 17:43:19 -0500
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3:987d73278bf9 4:158a71ee5733
1 <macros>
2 <xml name="generic_requirements">
3 <requirements>
4 <requirement type="package" version="3.0.9016">proteowizard</requirement>
5 </requirements>
6 </xml>
7 <token name="@VERSION@">3.0</token>
8
9 <xml name="msconvertCommand">
10 <command interpreter="python">
11 <![CDATA[
12 #import re
13 #set $ext = $input.ext
14 msconvert_wrapper.py
15 #if $ext == 'wiff':
16 #set basename = 'absciex'
17 #if hasattr($input, 'display_name')
18 #set basename = $re.sub('\W','_',$input.display_name)
19 #end if
20 --input=${input.extra_files_path}/wiff
21 --input_name='${basename}.wiff
22 --implicit=${input.extra_files_path}/wiff_scan
23 --input=${input.extra_files_path}/wiff_scan
24 --input_name='${basename}.wiff.scan
25 #else
26 --input=${input}
27 #if hasattr($input, 'display_name')
28 --input_name='${input.display_name}'
29 #end if
30 #end if
31 --output=${output}
32 ## BEGIN_VERSION_DEFAULT
33 --fromextension=$ext
34 ## END_VERSION_DEFAULT
35 --toextension=${output_type}
36
37 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
38 #if $data_processing.precursor_refinement.use_mzrefinement
39 #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name)
40 #if $data_processing.precursor_refinement.input_ident.ext == 'mzid':
41 #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name)
42 #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml':
43 #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name)
44 #end if
45 --ident=$data_processing.precursor_refinement.input_ident
46 --ident_name=$input_ident_name
47 --refinement=$output_refinement
48 --filter "mzRefiner $input_ident_name
49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
54 #end if
55
56 #if $data_processing.peak_picking.pick_peaks
57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
58 #end if
59
60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
61 --filter "chargeStatePredictor
62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
63 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
64 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
65 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
66 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
67 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
68 --filter "turbocharger
69 minCharge=$data_processing.charge_state_calculation.minCharge
70 maxCharge=$data_processing.charge_state_calculation.maxCharge
71 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
72 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
73 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
76 #end if
77
78 #for threshold_entry in $data_processing.thresholds
79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
80 #end for
81
82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
84 #end if
85
86 #if $data_processing.etd_filtering.do_etd_filtering
87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
88 $data_processing.etd_filtering.remove_charge_reduced
89 $data_processing.etd_filtering.remove_neutral_loss
90 $data_processing.etd_filtering.blanket_removal
91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
92 #end if
93
94 #if $data_processing.ms2denoise.denoise
95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
96 #end if
97
98 #if str($data_processing.ms2deisotope) == "true"
99 --filter "MS2Deisotope"
100 #end if
101
102
103 ## SCAN INCLUSION/EXCLUSION FILTERS
104 #if str($filtering.activation) != "false"
105 --filter "activation $filtering.activation"
106 #end if
107
108 #if len($filtering.indices) > 0
109 --filter "index
110 #for $index in $filtering.indices
111 [${index.from},${index.to}]
112 #end for
113 "
114 #end if
115
116 #if len($filtering.scan_numbers) > 0
117 --filter "scanNumber
118 #for $scan_number in $filtering.scan_numbers
119 [${scan_number.from},${scan_number.to}]
120 #end for
121 "
122 #end if
123
124 #if $filtering.strip_it.value
125 --filter "stripIT"
126 #end if
127
128 #if $filtering.filter_ms_levels.do_ms_level_filter
129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
130 #end if
131
132 #if str($filtering.polarity) != "false"
133 --filter "polarity $filtering.polarity"
134 #end if
135
136 #if str($filtering.analyzer) != "false"
137 --filter "analyzer $filtering.analyzer"
138 #end if
139
140 ## OUTPUT ENCODING
141 --
142 #set $mz_encoding = str($settings.mz_encoding)
143 #set $intensity_encoding = str($settings.intensity_encoding)
144 #if $mz_encoding == $intensity_encoding
145 #if $mz_encoding == "64"
146 --64
147 #else
148 --32
149 #end if
150 #else
151 --mz${mz_encoding}
152 --inten${intensity_encoding}
153 #end if
154
155 #set binary_compression = str($settings.binary_compression)
156 #if $binary_compression == "zlib"
157 --zlib
158 #else if $binary_compression == "numpressLinearPic"
159 --numpressLinear --numpressPic
160 #else if $binary_compression == "numpressLinearSlof"
161 --numpressLinear --numpressSlof
162 #else if $binary_compression == "numpressLinear"
163 --numpressLinear
164 #else if $binary_compression == "numpressPic"
165 --numpressPic
166 #else if $binary_compression == "numpressSlof"
167 --numpressSlof
168 #end if
169
170 #if $settings.gzip_compression
171 --gzip
172 #end if
173
174 ]]>
175 </command>
176 </xml>
177
178 <xml name="msconvertInputParameters">
179 <param name="output_type" type="select" label="Output Type">
180 <option value="mz5" selected="true">mz5</option>
181 <option value="mzML">mzML</option>
182 <option value="mzXML">mzXML</option>
183 <option value="mgf">mgf</option>
184 <option value="ms2">ms2</option>
185 </param>
186
187 <section name="data_processing" title="Data Processing Filters">
188
189 <conditional name="peak_picking">
190 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
191 <when value="false" />
192 <when value="true">
193 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
194 <option value="1">MS1 Only (1)</option>
195 <option value="2">MS2 Only (2)</option>
196 <option value="2-">MS2 and on (2-)</option>
197 <option value="1-" selected="true">All Levels (1-)</option>
198 </param>
199 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
200 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
201 <option value="cwt">CantWaiT - continuous wavelet transform</option>
202 </param>
203 </when>
204 </conditional>
205
206 <conditional name="precursor_refinement">
207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
208 <when value="false"></when>
209 <when value="true">
210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
211 <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+" />
212 <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." />
213 <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
214 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
215 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
216 <option value="1">MS1 Only (1)</option>
217 <option value="2">MS2 Only (2)</option>
218 <option value="2-">MS2 and on (2-)</option>
219 <option value="1-" selected="true">All Levels (1-)</option>
220 </param>
221 </when>
222 </conditional>
223
224 <conditional name="charge_state_calculation">
225 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
226 <option value="false">no</option>
227 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
228 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
229 </param>
230 <when value="false" />
231 <when value="predictor">
232 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
233 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
234 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
235 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
236 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
237 </when>
238 <when value="turbocharger">
239 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
240 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
241 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
242 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
243 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
244 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
245 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
246 </when>
247 </conditional>
248
249 <repeat name="thresholds" title="Filter by Threshold">
250 <param type="select" label="Specify threshold on" name="threshold_type" help="">
251 <option value="count">Peak count</option>
252 <option value="count-after-ties">Peak count (after ties)</option>
253 <option value="absolute">Peak absolute intensity</option>
254 <option value="bpi-relative">Fraction of base peak intensity</option>
255 <option value="tic-relative">Fraction of total ion current</option>
256 <option value="tic-fraction">Aggregate fraction of total ion current</option>
257 </param>
258 <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
259 <param type="select" label="Keep" name="orientation">
260 <option value="most-intense">Most intense peaks</option>
261 <option value="least-intense">Least intense peaks</option>
262 </param>
263 </repeat>
264
265 <conditional name="filter_mz_windows">
266 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
267 <when value="false" />
268 <when value="true">
269 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
270 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
271 </when>
272 </conditional>
273
274 <conditional name="etd_filtering">
275 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
276 <when value="false" />
277 <when value="true">
278 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
279 <option value="true" selected="true">yes</option>
280 <option value="false">no</option>
281 </param>
282 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
283 <option value="true" selected="true">yes</option>
284 <option value="false">no</option>
285 </param>
286 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
287 <option value="true" selected="true">yes</option>
288 <option value="false">no</option>
289 </param>
290 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
291 <option value="true" selected="true">yes</option>
292 <option value="false">no</option>
293 </param>
294 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
295 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
296 <option value="MZ" selected="true">mz</option>
297 <option value="PPM">ppm</option>
298 </param>
299 </when>
300 </conditional>
301
302 <conditional name="ms2denoise">
303 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
304 <when value="true">
305 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
306 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
307 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
308 </when>
309 <when value="false" />
310 </conditional>
311
312 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
313
314 </section>
315
316
317 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
318
319 <param name="activation" type="select" label="Filter by Activation">
320 <option value="false" selected="true">no</option>
321 <option value="ETD">ETD</option>
322 <option value="CID">CID</option>
323 <option value="SA">SA</option>
324 <option value="HCD">HCD</option>
325 <option value="BIRD">BIRD</option>
326 <option value="ECD">ECD</option>
327 <option value="IRMPD">IRMPD</option>
328 <option value="PD">PD</option>
329 <option value="PSD">PSD</option>
330 <option value="PQD">PQD</option>
331 <option value="SID">SID</option>
332 <option value="SORI">SORI</option>
333 </param>
334
335 <repeat name="indices" title="Filter Scan Indices">
336 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
337 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
338 </repeat>
339
340 <repeat name="scan_numbers" title="Filter Scan Numbers">
341 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
342 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
343 </repeat>
344
345 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
346
347 <conditional name="filter_ms_levels">
348 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
349 <when value="false" />
350 <when value="true">
351 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
352 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
353 </when>
354 </conditional>
355
356 <param name="polarity" type="select" label="Filter by Polarity">
357 <option value="false" selected="true">no</option>
358 <option value="positive">positive</option>
359 <option value="negative">negative</option>
360 </param>
361
362 <param name="analyzer" type="select" label="Filter by Analyzer">
363 <option value="false" selected="true">no</option>
364 <option value="quad">Quadrupole</option>
365 <option value="orbi">Orbitrap</option>
366 <option value="FT">Fourier-transform</option>
367 <option value="IT">Ion trap</option>
368 <option value="TOF">Time of flight</option>
369 </param>
370 </section>
371
372
373 <section name="settings" title="Output Encoding Settings">
374 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
375 <option value="64" selected="true">64</option>
376 <option value="32">32</option>
377 </param>
378 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
379 <option value="64">64</option>
380 <option value="32" selected="true">32</option>
381 </param>
382 <param type="select" name="binary_compression" label="Binary data compression">
383 <option value="false">None</option>
384 <option value="zlib" selected="true">zlib</option>
385 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
386 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
387 <option value="numpressLinear">numpressLinear only</option>
388 <option value="numpressPic">numpressPic only</option>
389 <option value="numpressSlof">numpressSlof only</option>
390 </param>
391 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
392 </section>
393 </xml>
394
395 <xml name="msconvertOutput">
396 <outputs>
397 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
398 <change_format>
399 <when input="output_type" value="mz5" format="mz5" />
400 <when input="output_type" value="mzXML" format="mzxml" />
401 <when input="output_type" value="ms2" format="ms2" />
402 <when input="output_type" value="mgf" format="mgf" />
403 </change_format>
404 </data>
405 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
406 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
407 </data>
408 </outputs>
409 </xml>
410
411
412 <xml name="msconvert_tests">
413 <test>
414 <param name="input" value="small.mzML" />
415 <param name="output_type" value="mzML" />
416 <param name="pick_peaks" value="true" />
417 <param name="pick_peaks_algorithm" value="cwt" />
418 <param name="pick_peaks_ms_levels" value="1-" />
419 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
420 </test>
421
422 <!-- this data file only has profile MS1, so the result is the same -->
423 <test>
424 <param name="input" value="small.mzML" />
425 <param name="output_type" value="mzML" />
426 <param name="pick_peaks" value="true" />
427 <param name="pick_peaks_algorithm" value="cwt" />
428 <param name="pick_peaks_ms_levels" value="1" />
429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
430 </test>
431 <test>
432 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
433 <param name="output_type" value="mz5" />
434 <param name="mz_encoding" value="64" />
435 <param name="intensity_encoding" value="64" />
436 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
437 </test>
438 <test>
439 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
440 <param name="output_type" value="mzXML" />
441 <param name="mz_encoding" value="32" />
442 <param name="intensity_encoding" value="32" />
443 <output name="output" file="small-zlib-32.mzXML" />
444 </test>
445 <!-- TODO: how to test gzipped output?
446 <test>
447 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
448 <param name="output_type" value="mzXML" />
449 <param name="mz_encoding" value="32" />
450 <param name="intensity_encoding" value="32" />
451 <param name="binary_compression" value="false" />
452 <param name="gzip_compression" value="true" />
453 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
454 </test>
455 <test>
456 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
457 <param name="output_type" value="mzML" />
458 <param name="mz_encoding" value="32" />
459 <param name="intensity_encoding" value="32" />
460 <param name="binary_compression" value="false" />
461 <param name="gzip_compression" value="true" />
462 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
463 </test>-->
464
465 <test>
466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
467 <param name="output_type" value="mzML" />
468 <param name="binary_compression" value="numpressLinearPic" />
469 <output name="output" file="small-numpressLP.mzML" />
470 </test>
471
472 <test>
473 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
474 <param name="output_type" value="mzML" />
475 <param name="binary_compression" value="numpressLinearSlof" />
476 <output name="output" file="small-numpressLS.mzML" />
477 </test>
478
479 <test>
480 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
481 <param name="output_type" value="mzML" />
482 <param name="binary_compression" value="numpressLinear" />
483 <output name="output" file="small-numpressL.mzML" />
484 </test>
485
486 <test>
487 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
488 <param name="output_type" value="mzML" />
489 <param name="binary_compression" value="numpressPic" />
490 <output name="output" file="small-numpressP.mzML" />
491 </test>
492
493 <test>
494 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
495 <param name="output_type" value="mzML" />
496 <param name="binary_compression" value="numpressSlof" />
497 <output name="output" file="small-numpressS.mzML" />
498 </test>
499
500 <test>
501 <param name="input" value="Rpal_01.mz5" />
502 <param name="output_type" value="mzML" />
503 <param name="binary_compression" value="numpressLinearPic" />
504 <param name="use_mzrefinement" value="true" />
505 <param name="input_ident" value="Rpal_01.pepXML.gz" />
506 <param name="thresholdScore" value="mvh" />
507 <param name="thresholdValue" value="40-" />
508 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
509 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
510 </test>
511
512 <test>
513 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
514 <param name="output_type" value="mzML" />
515 <param name="binary_compression" value="numpressLinearPic" />
516 <param name="charge_state_calculation_method" value="predictor" />
517 <param name="predictor_overrideExistingCharge" value="true" />
518 <param name="minMultipleCharge" value="2" />
519 <param name="maxMultipleCharge" value="5" />
520 <param name="singleChargeFractionTIC" value="0.95" />
521 <param name="maxKnownCharge" value="8" />
522 <output name="output" file="small-chargeStatePredictor.mzML" />
523 </test>
524 <test>
525 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
526 <param name="output_type" value="mzML" />
527 <param name="binary_compression" value="numpressLinearPic" />
528 <param name="charge_state_calculation_method" value="turbocharger" />
529 <param name="minCharge" value="1" />
530 <param name="maxCharge" value="5" />
531 <param name="precursorsBefore" value="1" />
532 <param name="precursorsAfter" value="1" />
533 <param name="halfIsoWidth" value="1.5" />
534 <param name="defaultMinCharge" value="1" />
535 <param name="defaultMaxCharge" value="5" />
536 <output name="output" file="small-turbocharger.mzML" />
537 </test>
538 <test>
539 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
540 <param name="output_type" value="mzML" />
541 <param name="do_etd_filtering" value="true" />
542 <param name="remove_precursor" value="true" />
543 <param name="remove_charge_reduced" value="true" />
544 <param name="remove_neutral_loss" value="false" />
545 <param name="blanket_removal" value="false" />
546 <param name="matching_tolerance" value="50" />
547 <param name="matching_tolerance_units" value="ppm" />
548 <param name="binary_compression" value="numpressLinearPic" />
549 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
550 </test>
551 <test>
552 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
553 <param name="output_type" value="mzML" />
554 <param name="thresholds_0|threshold_type" value="count" />
555 <param name="thresholds_0|value" value="100" />
556 <param name="thresholds_0|orientation" value="most-intense" />
557 <param name="thresholds_1|threshold_type" value="absolute" />
558 <param name="thresholds_1|value" value="1" />
559 <param name="thresholds_1|orientation" value="most-intense" />
560 <param name="binary_compression" value="numpressLinearPic" />
561 <output name="output" file="small-threshold.mzML" />
562 </test>
563 <test>
564 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
565 <param name="output_type" value="mzML" />
566 <param name="do_mzwindow_filter" value="true" />
567 <param name="mz_window_from" value="420" />
568 <param name="mz_window_to" value="840" />
569 <param name="binary_compression" value="numpressLinearPic" />
570 <output name="output" file="small-mzWindow.mzML" />
571 </test>
572 <test>
573 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
574 <param name="output_type" value="mzML" />
575 <param name="denoise" value="true" />
576 <param name="num_peaks" value="10" />
577 <param name="window_width" value="40" />
578 <param name="relax" value="false" />
579 <param name="binary_compression" value="numpressLinearPic" />
580 <output name="output" file="small-denoise.mzML" />
581 </test>
582 <test>
583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
584 <param name="output_type" value="mzML" />
585 <param name="ms2deisotope" value="true" />
586 <param name="binary_compression" value="numpressLinearPic" />
587 <output name="output" file="small-deisotope.mzML" />
588 </test>
589 <test>
590 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
591 <param name="output_type" value="mzML" />
592 <param name="activation" value="CID" />
593 <param name="binary_compression" value="numpressLinearPic" />
594 <output name="output" file="small-activation.mzML" />
595 </test>
596 <test>
597 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
598 <param name="output_type" value="mzML" />
599 <param name="indices_0|from" value="2" />
600 <param name="indices_0|to" value="4" />
601 <param name="indices_1|from" value="10" />
602 <param name="indices_1|to" value="10" />
603 <param name="indices_2|from" value="13" />
604 <param name="indices_2|to" value="15" />
605 <param name="binary_compression" value="numpressLinearPic" />
606 <output name="output" file="small-index-filter.mzML" />
607 </test>
608 <test>
609 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
610 <param name="output_type" value="mzML" />
611 <param name="strip_it" value="true" />
612 <param name="binary_compression" value="numpressLinearPic" />
613 <output name="output" file="small-strip-it.mzML" />
614 </test>
615 <test>
616 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
617 <param name="output_type" value="mzML" />
618 <param name="do_ms_level_filter" value="true" />
619 <param name="ms_level_from" value="2" />
620 <param name="ms_level_to" value="2" />
621 <param name="binary_compression" value="numpressLinearPic" />
622 <output name="output" file="small-ms-level-filter.mzML" />
623 </test>
624 <test>
625 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
626 <param name="output_type" value="mzML" />
627 <param name="polarity" value="positive" />
628 <param name="binary_compression" value="numpressLinearPic" />
629 <output name="output" file="small-polarity-filter.mzML" />
630 </test>
631 <test>
632 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
633 <param name="output_type" value="mzML" />
634 <param name="analyzer" value="IT" />
635 <param name="binary_compression" value="numpressLinearPic" />
636 <output name="output" file="small-analyzer-filter.mzML" />
637 </test>
638 <test>
639 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
640 <param name="output_type" value="mzML" />
641 <param name="scan_numbers_0|from" value="3" />
642 <param name="scan_numbers_0|to" value="5" />
643 <param name="scan_numbers_1|from" value="11" />
644 <param name="scan_numbers_1|to" value="11" />
645 <param name="scan_numbers_2|from" value="14" />
646 <param name="scan_numbers_2|to" value="16" />
647 <param name="binary_compression" value="numpressLinearPic" />
648 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
649 </test>
650 <!--<test>
651 <param name="input" value="small.mzML" />
652 <param name="output_type" value="mzML" />
653 <param name="binary_compression" value="numpressLinearPic" />
654 <output name="output" file="small-deisotope-poisson.mzML" />
655 </test>-->
656 </xml>
657 <xml name="msconvert_help">
658 **What it does**
659
660 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
661
662 You can view the original documentation here_.
663
664 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
665 </xml>
666
667 <xml name="citations">
668 <citations>
669 <citation type="doi">10.1093/bioinformatics/btn323</citation>
670 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
671 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
672 </citations>
673 </xml>
674
675 </macros>