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comparison msconvert3.xml @ 0:10f4a0356342

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author galaxyp
date Wed, 19 Dec 2012 00:10:08 -0500
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1 <tool id="msconvert3" name="msconvert3" version="0.1.0">
2 <!-- BEGIN_VERSION_DEFAULT -->
3 <description>Convert and filter a mass spec peak list</description>
4 <!-- END_VERSION_DEFAULT -->
5
6 <command interpreter="python">
7 msconvert_wrapper.py
8 --input=${input}
9 #if hasattr($input, 'display_name')
10 --input_name='${input.display_name}'
11 #end if
12 --output=${output}
13 ## BEGIN_VERSION_DEFAULT
14 --fromextension=${input.ext}
15 ## END_VERSION_DEFAULT
16
17
18 --toextension=${output_type}
19
20 #if $settings.settingsType == "full"
21 --binaryencoding=${settings.binary_encoding}
22 --mzencoding=${settings.mz_encoding}
23 --intensityencoding=${settings.intensity_encoding}
24 --zlib=${settings.zlib}
25 #end if
26
27 #if $filtering.filtering_use
28
29 #if $filtering.precursor_recalculation.value
30 --filter "precursorRecalculation"
31 #end if
32
33 #if $filtering.peak_picking.pick_peaks
34 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
35 #end if
36
37 #if str($filtering.activation) != "false"
38 --filter "activation $filtering.activation"
39 #end if
40
41 #if len($filtering.indices) > 0
42 --filter "index
43 #for $index in $filtering.indices
44 [${index.from},${index.to}]
45 #end for
46 "
47 #end if
48
49 #if len($filtering.scan_numbers) > 0
50 --filter "scanNumber
51 #for $scan_number in $filtering.scan_numbers
52 [${scan_number.from},${scan_number.to}]
53 #end for
54 "
55 #end if
56
57 #for threshold_entry in $filtering.threshold_repeat
58 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
59 #end for
60
61
62 #if $filtering.strip_it.value
63 --filter "stripIT"
64 #end if
65
66 #if $filtering.filter_mz_windows.do_filter
67 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
68 #end if
69
70
71 #if $filtering.filter_ms_levels.do_filter
72 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
73 #end if
74
75 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
76 --filter "ETDFilter"
77 #end if
78
79 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
80 --filter "ETDFilter removePrecursor:$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"
81 #end if
82
83 ## BEGIN_VERSION_3
84
85 #if $filtering.precursor_refine.value
86 --filter "precursorRefine"
87 #end if
88
89 #if $filtering.ms2denoise.denoise
90 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
91 #end if
92
93 #if str($filtering.ms2deisotope) == "true"
94 --filter "MS2Deisotope"
95 #end if
96
97 #if str($filtering.polarity) != "false"
98 --filter "polarity $filtering.polarity"
99 #end if
100
101 #if str($filtering.analyzer) != "false"
102 --filter "analyzer $filtering.analyzer"
103 #end if
104
105 ## END_VERSION_3
106
107 #end if
108
109 </command>
110
111 <inputs>
112
113 <!-- BEGIN_VERSION_DEFAULT -->
114 <conditional name="type">
115 <param name="input_type" type="select" label="Input Type">
116 <option value="mzml">mzML</option>
117 <option value="mzxml">mzXML</option>
118 <option value="mgf">mgf</option>
119 <option value="ms2">ms2</option>
120 </param>
121 <when value="mzml">
122 <param format="mzml" name="input" type="data" label="Input mzML"/>
123 </when>
124 <when value="mzxml">
125 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
126 </when>
127 <when value="mgf">
128 <param format="mgf" name="input" type="data" label="Input mgf"/>
129 </when>
130 <when value="ms2">
131 <param format="ms2" name="input" type="data" label="Input ms2"/>
132 </when>
133 </conditional>
134 <!-- END_VERSION_DEFAULT -->
135 <param name="output_type" type="select" label="Output Type">
136 <option value="mzML">mzML (indexed)</option>
137 <option value="unindexed_mzML">mzML (unindexed)</option>
138 <option value="mzXML">mzXML (indexed)</option>
139 <option value="unindexed_mzXML">mzXML (unindexed)</option>
140 <option value="mgf">mgf</option>
141 <option value="ms2">ms2</option>
142 </param>
143 <conditional name="filtering">
144 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
145 <when value="false" />
146 <when value="true">
147 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
148 <!-- BEGIN_VERSION_3 -->
149 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
150 <!-- END_VERSION_3 -->
151
152
153 <conditional name="peak_picking">
154 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
155 <when value="false" />
156 <when value="true">
157 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
158 <option value="1">MS1 Only (1)</option>
159 <option value="2">MS2 Only (2)</option>
160 <option value="2-">MS2 and on (2-)</option>
161 <option value="1-">All Levels (1-)</option>
162 </param>
163 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
164 </when>
165 </conditional>
166
167 <repeat name="threshold_repeat" title="Filter by Threshold">
168 <conditional name="threshold">
169 <param type="select" label="Specify threshold on" name="threshold_type" help="">
170 <option value="count">Peak count</option>
171 <option value="count-after-ties">Peak count (after ties)</option>
172 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
173 <option value="bpi-relative">Percent of base peak intensity</option>
174 <option value="tic-relative">Percent of total ion current</option>
175 <option value="tic-fraction">Aggregate percent of total ion current</option>
176 </param>
177 <when value="count">
178 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
179 </when>
180 <when value="count-after-ties">
181 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
182 </when>
183 <when value="absolute">
184 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
185 </when>
186 <when value="bpi-relative">
187 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
188 />
189 </when>
190 <when value="tic-relative">
191 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
192 />
193 </when>
194 <when value="tic-fraction">
195 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
196 </when>
197 </conditional>
198 <param type="select" label="Keep" name="orientation">
199 <option value="most-intense">Most intense peaks</option>
200 <option value="least-intense">Least intense peaks</option>
201 </param>
202 </repeat>
203
204
205 <param name="activation" type="select" label="Filter by Activation">
206 <option value="false" selected="true">no</option>
207 <option value="ETD">ETD</option>
208 <option value="CID">CID</option>
209 <option value="SA">SA</option>
210 <option value="HCD">HCD</option>
211 <!-- BEGIN_VERSION_3 -->
212 <option>BIRD</option>
213 <option>ECD</option>
214 <option>IRMPD</option>
215 <option>PD</option>
216 <option>PSD</option>
217 <option>PQD</option>
218 <option>SID</option>
219 <option>SORI</option>
220 <!-- END_VERSION_3 -->
221 </param>
222
223 <repeat name="indices" title="Filter Scan Indices">
224 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
225 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
226 </repeat>
227
228 <repeat name="scan_numbers" title="Filter Scan Numbers">
229 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
230 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
231 </repeat>
232
233 <conditional name="filter_mz_windows">
234 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
235 <when value="false" />
236 <when value="true">
237 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
238 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
239 </when>
240 </conditional>
241
242 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
243
244 <conditional name="filter_ms_levels">
245 <param name="do_filter" type="boolean" label="Filter MS Levels" />
246 <when value="false" />
247 <when value="true">
248 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
249 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
250 </when>
251 </conditional>
252
253 <conditional name="etd_filtering">
254 <param name="do_etd_filtering" type="select" label="ETD Filtering">
255 <option value="none" selected="true">none</option>
256 <option value="default">yes (with default options)</option>
257 <option value="advanced">yes (show advanced options) </option>
258 </param>
259 <when value="none" />
260 <when value="default" />
261 <when value="advanced">
262 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
263 </param>
264 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
265 <option value="MZ" selected="true">mz</option>
266 <option value="PPM">ppm</option>
267 </param>
268 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
269 <option value="true" selected="true">yes</option>
270 <option value="false">no</option>
271 </param>
272 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
273 <option value="true" selected="true">yes</option>
274 <option value="false">no</option>
275 </param>
276 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
277 <option value="true" selected="true">yes</option>
278 <option value="false">no</option>
279 </param>
280 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
281 <option value="true" selected="true">yes</option>
282 <option value="false">no</option>
283 </param>
284 </when>
285 </conditional>
286
287
288 <!-- BEGIN_VERSION_3 -->
289 <conditional name="ms2denoise">
290 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
291 <when value="true">
292 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
293 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
294 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
295 </when>
296 <when value="false" />
297 </conditional>
298 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
299
300 <param name="polarity" type="select" label="Filter by Polarity">
301 <option value="false" selected="true">no</option>
302 <option value="positive">positive</option>
303 <option value="negative">negative</option>
304 </param>
305
306 <param name="analyzer" type="select" label="Filter by Analyzer">
307 <option value="false" selected="true">no</option>
308 <option value="quad">quad</option>
309 <option value="orbi">orbi</option>
310 <option value="FT">FT</option>
311 <option value="IT">IT</option>
312 <option value="TOF">TOF</option>
313 </param>
314 <!-- END_VERSION_3 -->
315 </when>
316 </conditional>
317
318 <conditional name="settings">
319 <param name="settingsType" type="select" label="Advanced Settings" help="">
320 <option value="default">Use Defaults</option>
321 <option value="full">Full Parameter List</option>
322 </param>
323 <when value="default" />
324 <when value="full">
325 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
326 <option value="64" selected="true">64</option>
327 <option value="32">32</option>
328 </param>
329 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
330 <option value="64" selected="true">64</option>
331 <option value="32">32</option>
332 </param>
333 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
334 <option value="64">64</option>
335 <option value="32" selected="true">32</option>
336 </param>
337 <param type="boolean" name="zlib" label="Use zlib">
338 </param>
339 </when>
340 </conditional>
341
342
343 </inputs>
344 <outputs>
345 <data format="mzml" name="output">
346 <change_format>
347 <when input="output_type" value="mzXML" format="mzxml" />
348 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
349 <when input="output_type" value="ms2" format="ms2" />
350 <when input="output_type" value="mgf" format="mgf" />
351 </change_format>
352 </data>
353 </outputs>
354
355 <requirements>
356 <requirement type="package">proteowizard</requirement>
357 </requirements>
358
359 <help>
360 **What it does**
361
362 Converts between various mass spectrometry peak list representations. 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/galaxyp-toolshed-msconvert
375
376 </help>
377 </tool>