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comparison msconvert3_raw.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_raw" name="msconvert3_raw" version="0.1.0">
2 <!-- BEGIN_VERSION_RAW -->
3 <description>Convert and filter a Thermo Finnigan RAW file</description>
4 <!-- END_VERSION_RAW -->
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
14 ## BEGIN_VERSION_RAW
15 --fromextension=RAW
16 ## END_VERSION_RAW
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 <!-- BEGIN_VERSION_RAW -->
113 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
114 <!-- END_VERSION_RAW -->
115
116 <param name="output_type" type="select" label="Output Type">
117 <option value="mzML">mzML (indexed)</option>
118 <option value="unindexed_mzML">mzML (unindexed)</option>
119 <option value="mzXML">mzXML (indexed)</option>
120 <option value="unindexed_mzXML">mzXML (unindexed)</option>
121 <option value="mgf">mgf</option>
122 <option value="ms2">ms2</option>
123 </param>
124 <conditional name="filtering">
125 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
126 <when value="false" />
127 <when value="true">
128 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
129 <!-- BEGIN_VERSION_3 -->
130 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
131 <!-- END_VERSION_3 -->
132
133
134 <conditional name="peak_picking">
135 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
136 <when value="false" />
137 <when value="true">
138 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
139 <option value="1">MS1 Only (1)</option>
140 <option value="2">MS2 Only (2)</option>
141 <option value="2-">MS2 and on (2-)</option>
142 <option value="1-">All Levels (1-)</option>
143 </param>
144 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
145 </when>
146 </conditional>
147
148 <repeat name="threshold_repeat" title="Filter by Threshold">
149 <conditional name="threshold">
150 <param type="select" label="Specify threshold on" name="threshold_type" help="">
151 <option value="count">Peak count</option>
152 <option value="count-after-ties">Peak count (after ties)</option>
153 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
154 <option value="bpi-relative">Percent of base peak intensity</option>
155 <option value="tic-relative">Percent of total ion current</option>
156 <option value="tic-fraction">Aggregate percent of total ion current</option>
157 </param>
158 <when value="count">
159 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
160 </when>
161 <when value="count-after-ties">
162 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
163 </when>
164 <when value="absolute">
165 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
166 </when>
167 <when value="bpi-relative">
168 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
169 />
170 </when>
171 <when value="tic-relative">
172 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
173 />
174 </when>
175 <when value="tic-fraction">
176 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
177 </when>
178 </conditional>
179 <param type="select" label="Keep" name="orientation">
180 <option value="most-intense">Most intense peaks</option>
181 <option value="least-intense">Least intense peaks</option>
182 </param>
183 </repeat>
184
185
186 <param name="activation" type="select" label="Filter by Activation">
187 <option value="false" selected="true">no</option>
188 <option value="ETD">ETD</option>
189 <option value="CID">CID</option>
190 <option value="SA">SA</option>
191 <option value="HCD">HCD</option>
192 <!-- BEGIN_VERSION_3 -->
193 <option>BIRD</option>
194 <option>ECD</option>
195 <option>IRMPD</option>
196 <option>PD</option>
197 <option>PSD</option>
198 <option>PQD</option>
199 <option>SID</option>
200 <option>SORI</option>
201 <!-- END_VERSION_3 -->
202 </param>
203
204 <repeat name="indices" title="Filter Scan Indices">
205 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
206 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
207 </repeat>
208
209 <repeat name="scan_numbers" title="Filter Scan Numbers">
210 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
211 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
212 </repeat>
213
214 <conditional name="filter_mz_windows">
215 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
216 <when value="false" />
217 <when value="true">
218 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
219 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
220 </when>
221 </conditional>
222
223 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
224
225 <conditional name="filter_ms_levels">
226 <param name="do_filter" type="boolean" label="Filter MS Levels" />
227 <when value="false" />
228 <when value="true">
229 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
230 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
231 </when>
232 </conditional>
233
234 <conditional name="etd_filtering">
235 <param name="do_etd_filtering" type="select" label="ETD Filtering">
236 <option value="none" selected="true">none</option>
237 <option value="default">yes (with default options)</option>
238 <option value="advanced">yes (show advanced options) </option>
239 </param>
240 <when value="none" />
241 <when value="default" />
242 <when value="advanced">
243 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
244 </param>
245 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
246 <option value="MZ" selected="true">mz</option>
247 <option value="PPM">ppm</option>
248 </param>
249 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
250 <option value="true" selected="true">yes</option>
251 <option value="false">no</option>
252 </param>
253 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
254 <option value="true" selected="true">yes</option>
255 <option value="false">no</option>
256 </param>
257 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
258 <option value="true" selected="true">yes</option>
259 <option value="false">no</option>
260 </param>
261 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
262 <option value="true" selected="true">yes</option>
263 <option value="false">no</option>
264 </param>
265 </when>
266 </conditional>
267
268
269 <!-- BEGIN_VERSION_3 -->
270 <conditional name="ms2denoise">
271 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
272 <when value="true">
273 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
274 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
275 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
276 </when>
277 <when value="false" />
278 </conditional>
279 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
280
281 <param name="polarity" type="select" label="Filter by Polarity">
282 <option value="false" selected="true">no</option>
283 <option value="positive">positive</option>
284 <option value="negative">negative</option>
285 </param>
286
287 <param name="analyzer" type="select" label="Filter by Analyzer">
288 <option value="false" selected="true">no</option>
289 <option value="quad">quad</option>
290 <option value="orbi">orbi</option>
291 <option value="FT">FT</option>
292 <option value="IT">IT</option>
293 <option value="TOF">TOF</option>
294 </param>
295 <!-- END_VERSION_3 -->
296 </when>
297 </conditional>
298
299 <conditional name="settings">
300 <param name="settingsType" type="select" label="Advanced Settings" help="">
301 <option value="default">Use Defaults</option>
302 <option value="full">Full Parameter List</option>
303 </param>
304 <when value="default" />
305 <when value="full">
306 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
307 <option value="64" selected="true">64</option>
308 <option value="32">32</option>
309 </param>
310 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
311 <option value="64" selected="true">64</option>
312 <option value="32">32</option>
313 </param>
314 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
315 <option value="64">64</option>
316 <option value="32" selected="true">32</option>
317 </param>
318 <param type="boolean" name="zlib" label="Use zlib">
319 </param>
320 </when>
321 </conditional>
322
323
324 </inputs>
325 <outputs>
326 <data format="mzml" name="output">
327 <change_format>
328 <when input="output_type" value="mzXML" format="mzxml" />
329 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
330 <when input="output_type" value="ms2" format="ms2" />
331 <when input="output_type" value="mgf" format="mgf" />
332 </change_format>
333 </data>
334 </outputs>
335
336 <requirements>
337 <requirement type="package">proteowizard</requirement>
338 </requirements>
339
340 <help>
341 **What it does**
342
343 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
344
345 You can view the original documentation here_.
346
347 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
348
349 ------
350
351 **Citation**
352
353 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.`
354
355 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
356
357 </help>
358 </tool>