|
8
|
1 <tool id="msconvert" name="msconvert" version="0.3.0">
|
|
|
2 <!-- BEGIN_VERSION_DEFAULT -->
|
|
|
3 <description>Convert and filter a mass spec peak list</description>
|
|
|
4 <!-- END_VERSION_DEFAULT -->
|
|
|
5 <!--
|
|
|
6 <requirements>
|
|
|
7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
|
|
|
8 </requirements>
|
|
|
9 -->
|
|
|
10 <command interpreter="python">
|
|
|
11 #set $ext = $input.ext
|
|
|
12 msconvert_wrapper.py
|
|
|
13 --input=${input}
|
|
|
14 #if hasattr($input, 'display_name')
|
|
|
15 --input_name='${input.display_name}'
|
|
|
16 #end if
|
|
|
17 --output=${output}
|
|
|
18 ## BEGIN_VERSION_DEFAULT
|
|
|
19 --fromextension=$ext
|
|
|
20 ## END_VERSION_DEFAULT
|
|
|
21
|
|
|
22
|
|
|
23 --toextension=${output_type}
|
|
|
24
|
|
|
25 #if $settings.settingsType == "full"
|
|
|
26 --binaryencoding=${settings.binary_encoding}
|
|
|
27 --mzencoding=${settings.mz_encoding}
|
|
|
28 --intensityencoding=${settings.intensity_encoding}
|
|
|
29 --zlib=${settings.zlib}
|
|
|
30 #end if
|
|
|
31
|
|
|
32 #if $filtering.filtering_use
|
|
|
33
|
|
|
34 #if $filtering.precursor_recalculation.value
|
|
|
35 --filter "precursorRecalculation"
|
|
|
36 #end if
|
|
|
37
|
|
|
38 #if $filtering.peak_picking.pick_peaks
|
|
|
39 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
|
|
|
40 #end if
|
|
|
41
|
|
|
42 #if str($filtering.activation) != "false"
|
|
|
43 --filter "activation $filtering.activation"
|
|
|
44 #end if
|
|
|
45
|
|
|
46 #if len($filtering.indices) > 0
|
|
|
47 --filter "index
|
|
|
48 #for $index in $filtering.indices
|
|
|
49 [${index.from},${index.to}]
|
|
|
50 #end for
|
|
|
51 "
|
|
|
52 #end if
|
|
|
53
|
|
|
54 #if len($filtering.scan_numbers) > 0
|
|
|
55 --filter "scanNumber
|
|
|
56 #for $scan_number in $filtering.scan_numbers
|
|
|
57 [${scan_number.from},${scan_number.to}]
|
|
|
58 #end for
|
|
|
59 "
|
|
|
60 #end if
|
|
|
61
|
|
|
62 #for threshold_entry in $filtering.threshold_repeat
|
|
|
63 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
|
|
|
64 #end for
|
|
|
65
|
|
|
66
|
|
|
67 #if $filtering.strip_it.value
|
|
|
68 --filter "stripIT"
|
|
|
69 #end if
|
|
|
70
|
|
|
71 #if $filtering.filter_mz_windows.do_filter
|
|
|
72 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
|
|
|
73 #end if
|
|
|
74
|
|
|
75
|
|
|
76 #if $filtering.filter_ms_levels.do_filter
|
|
|
77 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
|
|
|
78 #end if
|
|
|
79
|
|
|
80 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
|
|
|
81 --filter "ETDFilter"
|
|
|
82 #end if
|
|
|
83
|
|
|
84 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
|
|
|
85 --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
|
|
|
86 #end if
|
|
|
87
|
|
|
88 ## BEGIN_VERSION_3
|
|
|
89
|
|
|
90 #if $filtering.precursor_refine.value
|
|
|
91 --filter "precursorRefine"
|
|
|
92 #end if
|
|
|
93
|
|
|
94 #if $filtering.ms2denoise.denoise
|
|
|
95 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
|
|
|
96 #end if
|
|
|
97
|
|
|
98 #if str($filtering.ms2deisotope) == "true"
|
|
|
99 --filter "MS2Deisotope"
|
|
|
100 #end if
|
|
|
101
|
|
|
102 #if str($filtering.polarity) != "false"
|
|
|
103 --filter "polarity $filtering.polarity"
|
|
|
104 #end if
|
|
|
105
|
|
|
106 #if str($filtering.analyzer) != "false"
|
|
|
107 --filter "analyzer $filtering.analyzer"
|
|
|
108 #end if
|
|
|
109
|
|
|
110 ## END_VERSION_3
|
|
|
111
|
|
|
112 #end if
|
|
|
113
|
|
|
114 </command>
|
|
|
115
|
|
|
116 <inputs>
|
|
|
117
|
|
|
118 <!-- BEGIN_VERSION_DEFAULT -->
|
|
|
119 <conditional name="type">
|
|
|
120 <param name="input_type" type="select" label="Input Type">
|
|
|
121 <option value="mzml">mzML</option>
|
|
|
122 <option value="mzxml">mzXML</option>
|
|
|
123 <option value="mgf">mgf</option>
|
|
|
124 <option value="ms2">ms2</option>
|
|
|
125 </param>
|
|
|
126 <when value="mzml">
|
|
|
127 <param format="mzml" name="input" type="data" label="Input mzML"/>
|
|
|
128 </when>
|
|
|
129 <when value="mzxml">
|
|
|
130 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
|
|
|
131 </when>
|
|
|
132 <when value="mgf">
|
|
|
133 <param format="mgf" name="input" type="data" label="Input mgf"/>
|
|
|
134 </when>
|
|
|
135 <when value="ms2">
|
|
|
136 <param format="ms2" name="input" type="data" label="Input ms2"/>
|
|
|
137 </when>
|
|
|
138 </conditional>
|
|
|
139 <!-- END_VERSION_DEFAULT -->
|
|
|
140 <param name="output_type" type="select" label="Output Type">
|
|
|
141 <option value="mzML">mzML (indexed)</option>
|
|
|
142 <option value="unindexed_mzML">mzML (unindexed)</option>
|
|
|
143 <option value="mzXML">mzXML (indexed)</option>
|
|
|
144 <option value="unindexed_mzXML">mzXML (unindexed)</option>
|
|
|
145 <option value="mgf">mgf</option>
|
|
|
146 <option value="ms2">ms2</option>
|
|
|
147 </param>
|
|
|
148 <conditional name="filtering">
|
|
|
149 <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
|
|
|
150 <when value="false" />
|
|
|
151 <when value="true">
|
|
|
152 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
|
|
|
153 <!-- BEGIN_VERSION_3 -->
|
|
|
154 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
|
|
|
155 <!-- END_VERSION_3 -->
|
|
|
156
|
|
|
157
|
|
|
158 <conditional name="peak_picking">
|
|
|
159 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
|
|
|
160 <when value="false" />
|
|
|
161 <when value="true">
|
|
|
162 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
|
|
|
163 <option value="1">MS1 Only (1)</option>
|
|
|
164 <option value="2">MS2 Only (2)</option>
|
|
|
165 <option value="2-">MS2 and on (2-)</option>
|
|
|
166 <option value="1-">All Levels (1-)</option>
|
|
|
167 </param>
|
|
|
168 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
|
|
|
169 </when>
|
|
|
170 </conditional>
|
|
|
171
|
|
|
172 <repeat name="threshold_repeat" title="Filter by Threshold">
|
|
|
173 <conditional name="threshold">
|
|
|
174 <param type="select" label="Specify threshold on" name="threshold_type" help="">
|
|
|
175 <option value="count">Peak count</option>
|
|
|
176 <option value="count-after-ties">Peak count (after ties)</option>
|
|
|
177 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
|
|
|
178 <option value="bpi-relative">Percent of base peak intensity</option>
|
|
|
179 <option value="tic-relative">Percent of total ion current</option>
|
|
|
180 <option value="tic-fraction">Aggregate percent of total ion current</option>
|
|
|
181 </param>
|
|
|
182 <when value="count">
|
|
|
183 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
|
|
|
184 </when>
|
|
|
185 <when value="count-after-ties">
|
|
|
186 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
|
|
|
187 </when>
|
|
|
188 <when value="absolute">
|
|
|
189 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
|
|
|
190 </when>
|
|
|
191 <when value="bpi-relative">
|
|
|
192 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
|
|
|
193 />
|
|
|
194 </when>
|
|
|
195 <when value="tic-relative">
|
|
|
196 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
|
|
|
197 />
|
|
|
198 </when>
|
|
|
199 <when value="tic-fraction">
|
|
|
200 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
|
|
|
201 </when>
|
|
|
202 </conditional>
|
|
|
203 <param type="select" label="Keep" name="orientation">
|
|
|
204 <option value="most-intense">Most intense peaks</option>
|
|
|
205 <option value="least-intense">Least intense peaks</option>
|
|
|
206 </param>
|
|
|
207 </repeat>
|
|
|
208
|
|
|
209
|
|
|
210 <param name="activation" type="select" label="Filter by Activation">
|
|
|
211 <option value="false" selected="true">no</option>
|
|
|
212 <option value="ETD">ETD</option>
|
|
|
213 <option value="CID">CID</option>
|
|
|
214 <option value="SA">SA</option>
|
|
|
215 <option value="HCD">HCD</option>
|
|
|
216 <!-- BEGIN_VERSION_3 -->
|
|
|
217 <option>BIRD</option>
|
|
|
218 <option>ECD</option>
|
|
|
219 <option>IRMPD</option>
|
|
|
220 <option>PD</option>
|
|
|
221 <option>PSD</option>
|
|
|
222 <option>PQD</option>
|
|
|
223 <option>SID</option>
|
|
|
224 <option>SORI</option>
|
|
|
225 <!-- END_VERSION_3 -->
|
|
|
226 </param>
|
|
|
227
|
|
|
228 <repeat name="indices" title="Filter Scan Indices">
|
|
|
229 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
|
|
|
230 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
|
|
|
231 </repeat>
|
|
|
232
|
|
|
233 <repeat name="scan_numbers" title="Filter Scan Numbers">
|
|
|
234 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
|
|
|
235 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
|
|
|
236 </repeat>
|
|
|
237
|
|
|
238 <conditional name="filter_mz_windows">
|
|
|
239 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
|
|
|
240 <when value="false" />
|
|
|
241 <when value="true">
|
|
|
242 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
|
|
|
243 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
|
|
|
244 </when>
|
|
|
245 </conditional>
|
|
|
246
|
|
|
247 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
|
|
|
248
|
|
|
249 <conditional name="filter_ms_levels">
|
|
|
250 <param name="do_filter" type="boolean" label="Filter MS Levels" />
|
|
|
251 <when value="false" />
|
|
|
252 <when value="true">
|
|
|
253 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
|
|
|
254 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
|
|
|
255 </when>
|
|
|
256 </conditional>
|
|
|
257
|
|
|
258 <conditional name="etd_filtering">
|
|
|
259 <param name="do_etd_filtering" type="select" label="ETD Filtering">
|
|
|
260 <option value="none" selected="true">none</option>
|
|
|
261 <option value="default">yes (with default options)</option>
|
|
|
262 <option value="advanced">yes (show advanced options) </option>
|
|
|
263 </param>
|
|
|
264 <when value="none" />
|
|
|
265 <when value="default" />
|
|
|
266 <when value="advanced">
|
|
|
267 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
|
|
|
268 </param>
|
|
|
269 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
|
|
|
270 <option value="MZ" selected="true">mz</option>
|
|
|
271 <option value="PPM">ppm</option>
|
|
|
272 </param>
|
|
|
273 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
|
|
|
274 <option value="true" selected="true">yes</option>
|
|
|
275 <option value="false">no</option>
|
|
|
276 </param>
|
|
|
277 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
|
|
|
278 <option value="true" selected="true">yes</option>
|
|
|
279 <option value="false">no</option>
|
|
|
280 </param>
|
|
|
281 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
|
|
|
282 <option value="true" selected="true">yes</option>
|
|
|
283 <option value="false">no</option>
|
|
|
284 </param>
|
|
|
285 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
|
|
|
286 <option value="true" selected="true">yes</option>
|
|
|
287 <option value="false">no</option>
|
|
|
288 </param>
|
|
|
289 </when>
|
|
|
290 </conditional>
|
|
|
291
|
|
|
292
|
|
|
293 <!-- BEGIN_VERSION_3 -->
|
|
|
294 <conditional name="ms2denoise">
|
|
|
295 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
|
|
|
296 <when value="true">
|
|
|
297 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
|
|
|
298 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
|
|
|
299 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
|
|
|
300 </when>
|
|
|
301 <when value="false" />
|
|
|
302 </conditional>
|
|
|
303 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
|
|
|
304
|
|
|
305 <param name="polarity" type="select" label="Filter by Polarity">
|
|
|
306 <option value="false" selected="true">no</option>
|
|
|
307 <option value="positive">positive</option>
|
|
|
308 <option value="negative">negative</option>
|
|
|
309 </param>
|
|
|
310
|
|
|
311 <param name="analyzer" type="select" label="Filter by Analyzer">
|
|
|
312 <option value="false" selected="true">no</option>
|
|
|
313 <option value="quad">quad</option>
|
|
|
314 <option value="orbi">orbi</option>
|
|
|
315 <option value="FT">FT</option>
|
|
|
316 <option value="IT">IT</option>
|
|
|
317 <option value="TOF">TOF</option>
|
|
|
318 </param>
|
|
|
319 <!-- END_VERSION_3 -->
|
|
|
320 </when>
|
|
|
321 </conditional>
|
|
|
322
|
|
|
323 <conditional name="settings">
|
|
|
324 <param name="settingsType" type="select" label="Advanced Settings" help="">
|
|
|
325 <option value="default">Use Defaults</option>
|
|
|
326 <option value="full">Full Parameter List</option>
|
|
|
327 </param>
|
|
|
328 <when value="default" />
|
|
|
329 <when value="full">
|
|
|
330 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
|
|
|
331 <option value="64" selected="true">64</option>
|
|
|
332 <option value="32">32</option>
|
|
|
333 </param>
|
|
|
334 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
|
|
|
335 <option value="64" selected="true">64</option>
|
|
|
336 <option value="32">32</option>
|
|
|
337 </param>
|
|
|
338 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
|
|
|
339 <option value="64">64</option>
|
|
|
340 <option value="32" selected="true">32</option>
|
|
|
341 </param>
|
|
|
342 <param type="boolean" name="zlib" label="Use zlib">
|
|
|
343 </param>
|
|
|
344 </when>
|
|
|
345 </conditional>
|
|
|
346
|
|
|
347
|
|
|
348 </inputs>
|
|
|
349 <outputs>
|
|
|
350 <data format="mzml" name="output">
|
|
|
351 <change_format>
|
|
|
352 <when input="output_type" value="mzXML" format="mzxml" />
|
|
|
353 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
|
|
|
354 <when input="output_type" value="ms2" format="ms2" />
|
|
|
355 <when input="output_type" value="mgf" format="mgf" />
|
|
|
356 </change_format>
|
|
|
357 </data>
|
|
|
358 </outputs>
|
|
|
359 <help>
|
|
|
360 **What it does**
|
|
|
361
|
|
|
362 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
|
|
|
363
|
|
|
364 You can view the original documentation here_.
|
|
|
365
|
|
|
366 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
|
|
|
367
|
|
|
368 ------
|
|
|
369
|
|
|
370 **Citation**
|
|
|
371
|
|
|
372 For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
|
|
|
373
|
|
|
374 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert
|
|
|
375
|
|
|
376 </help>
|
|
|
377 </tool>
|
