Mercurial > repos > galaxyp > msconvert
annotate msconvert3_raw.xml @ 5:08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 17 Feb 2014 08:13:33 -0600 |
parents | 001e77708ec9 |
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rev | line source |
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Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
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1 <tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.1"> |
0 | 2 <!-- BEGIN_VERSION_RAW --> |
3 <description>Convert and filter a Thermo Finnigan RAW file</description> | |
4 <!-- END_VERSION_RAW --> | |
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Bjoern: remove unused repository dependency, cleanups
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5 <requirements> |
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Bjoern: remove unused repository dependency, cleanups
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6 <requirement type="package">proteowizard</requirement> |
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Bjoern: remove unused repository dependency, cleanups
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7 <!-- BEGIN_VERSION_RAW --> |
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Bjoern: remove unused repository dependency, cleanups
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8 <requirement type="platform">windows</requirement> |
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Bjoern: remove unused repository dependency, cleanups
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9 <!-- END_VERSION_RAW --> |
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Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
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10 </requirements> |
0 | 11 <command interpreter="python"> |
3 | 12 #set $ext = $input.ext |
13 #if $ext.startswith("m:") | |
14 #set $ext = $ext[len("m:"):] | |
15 #end if | |
0 | 16 msconvert_wrapper.py |
17 --input=${input} | |
18 #if hasattr($input, 'display_name') | |
19 --input_name='${input.display_name}' | |
20 #end if | |
21 --output=${output} | |
22 | |
23 ## BEGIN_VERSION_RAW | |
24 --fromextension=RAW | |
25 ## END_VERSION_RAW | |
26 | |
27 --toextension=${output_type} | |
28 | |
29 #if $settings.settingsType == "full" | |
30 --binaryencoding=${settings.binary_encoding} | |
31 --mzencoding=${settings.mz_encoding} | |
32 --intensityencoding=${settings.intensity_encoding} | |
33 --zlib=${settings.zlib} | |
34 #end if | |
35 | |
36 #if $filtering.filtering_use | |
37 | |
38 #if $filtering.precursor_recalculation.value | |
39 --filter "precursorRecalculation" | |
40 #end if | |
41 | |
42 #if $filtering.peak_picking.pick_peaks | |
43 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" | |
44 #end if | |
45 | |
46 #if str($filtering.activation) != "false" | |
47 --filter "activation $filtering.activation" | |
48 #end if | |
49 | |
50 #if len($filtering.indices) > 0 | |
51 --filter "index | |
52 #for $index in $filtering.indices | |
53 [${index.from},${index.to}] | |
54 #end for | |
55 " | |
56 #end if | |
57 | |
58 #if len($filtering.scan_numbers) > 0 | |
59 --filter "scanNumber | |
60 #for $scan_number in $filtering.scan_numbers | |
61 [${scan_number.from},${scan_number.to}] | |
62 #end for | |
63 " | |
64 #end if | |
65 | |
66 #for threshold_entry in $filtering.threshold_repeat | |
67 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" | |
68 #end for | |
69 | |
70 | |
71 #if $filtering.strip_it.value | |
72 --filter "stripIT" | |
73 #end if | |
74 | |
75 #if $filtering.filter_mz_windows.do_filter | |
76 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" | |
77 #end if | |
78 | |
79 | |
80 #if $filtering.filter_ms_levels.do_filter | |
81 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" | |
82 #end if | |
83 | |
84 #if str($filtering.etd_filtering.do_etd_filtering) == "default" | |
85 --filter "ETDFilter" | |
86 #end if | |
87 | |
88 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" | |
89 --filter "ETDFilter removePrecursor:$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" | |
90 #end if | |
91 | |
92 ## BEGIN_VERSION_3 | |
93 | |
94 #if $filtering.precursor_refine.value | |
95 --filter "precursorRefine" | |
96 #end if | |
97 | |
98 #if $filtering.ms2denoise.denoise | |
99 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax" | |
100 #end if | |
101 | |
102 #if str($filtering.ms2deisotope) == "true" | |
103 --filter "MS2Deisotope" | |
104 #end if | |
105 | |
106 #if str($filtering.polarity) != "false" | |
107 --filter "polarity $filtering.polarity" | |
108 #end if | |
109 | |
110 #if str($filtering.analyzer) != "false" | |
111 --filter "analyzer $filtering.analyzer" | |
112 #end if | |
113 | |
114 ## END_VERSION_3 | |
115 | |
116 #end if | |
117 | |
118 </command> | |
119 | |
120 <inputs> | |
121 <!-- BEGIN_VERSION_RAW --> | |
4 | 122 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> |
0 | 123 <!-- END_VERSION_RAW --> |
124 | |
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08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
125 <param name="output_type" type="select" label="Output Type"> |
0 | 126 <option value="mzML">mzML (indexed)</option> |
127 <option value="unindexed_mzML">mzML (unindexed)</option> | |
128 <option value="mzXML">mzXML (indexed)</option> | |
129 <option value="unindexed_mzXML">mzXML (unindexed)</option> | |
130 <option value="mgf">mgf</option> | |
131 <option value="ms2">ms2</option> | |
132 </param> | |
133 <conditional name="filtering"> | |
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08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
134 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> |
0 | 135 <when value="false" /> |
136 <when value="true"> | |
137 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> | |
138 <!-- BEGIN_VERSION_3 --> | |
139 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> | |
140 <!-- END_VERSION_3 --> | |
141 | |
142 | |
143 <conditional name="peak_picking"> | |
144 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> | |
145 <when value="false" /> | |
146 <when value="true"> | |
147 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> | |
148 <option value="1">MS1 Only (1)</option> | |
149 <option value="2">MS2 Only (2)</option> | |
150 <option value="2-">MS2 and on (2-)</option> | |
151 <option value="1-">All Levels (1-)</option> | |
152 </param> | |
153 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> | |
154 </when> | |
155 </conditional> | |
156 | |
157 <repeat name="threshold_repeat" title="Filter by Threshold"> | |
158 <conditional name="threshold"> | |
159 <param type="select" label="Specify threshold on" name="threshold_type" help=""> | |
160 <option value="count">Peak count</option> | |
161 <option value="count-after-ties">Peak count (after ties)</option> | |
162 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> | |
163 <option value="bpi-relative">Percent of base peak intensity</option> | |
164 <option value="tic-relative">Percent of total ion current</option> | |
165 <option value="tic-fraction">Aggregate percent of total ion current</option> | |
166 </param> | |
167 <when value="count"> | |
168 <param type="integer" name="value" label="Number of peaks to keep" value="100" /> | |
169 </when> | |
170 <when value="count-after-ties"> | |
171 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> | |
172 </when> | |
173 <when value="absolute"> | |
174 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> | |
175 </when> | |
176 <when value="bpi-relative"> | |
177 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" | |
178 /> | |
179 </when> | |
180 <when value="tic-relative"> | |
181 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" | |
182 /> | |
183 </when> | |
184 <when value="tic-fraction"> | |
185 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> | |
186 </when> | |
187 </conditional> | |
188 <param type="select" label="Keep" name="orientation"> | |
189 <option value="most-intense">Most intense peaks</option> | |
190 <option value="least-intense">Least intense peaks</option> | |
191 </param> | |
192 </repeat> | |
193 | |
194 | |
195 <param name="activation" type="select" label="Filter by Activation"> | |
196 <option value="false" selected="true">no</option> | |
197 <option value="ETD">ETD</option> | |
198 <option value="CID">CID</option> | |
199 <option value="SA">SA</option> | |
200 <option value="HCD">HCD</option> | |
201 <!-- BEGIN_VERSION_3 --> | |
202 <option>BIRD</option> | |
203 <option>ECD</option> | |
204 <option>IRMPD</option> | |
205 <option>PD</option> | |
206 <option>PSD</option> | |
207 <option>PQD</option> | |
208 <option>SID</option> | |
209 <option>SORI</option> | |
210 <!-- END_VERSION_3 --> | |
211 </param> | |
212 | |
213 <repeat name="indices" title="Filter Scan Indices"> | |
214 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> | |
215 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> | |
216 </repeat> | |
217 | |
218 <repeat name="scan_numbers" title="Filter Scan Numbers"> | |
219 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> | |
220 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> | |
221 </repeat> | |
222 | |
223 <conditional name="filter_mz_windows"> | |
224 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> | |
225 <when value="false" /> | |
226 <when value="true"> | |
227 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> | |
228 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> | |
229 </when> | |
230 </conditional> | |
231 | |
232 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> | |
233 | |
234 <conditional name="filter_ms_levels"> | |
235 <param name="do_filter" type="boolean" label="Filter MS Levels" /> | |
236 <when value="false" /> | |
237 <when value="true"> | |
238 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> | |
239 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> | |
240 </when> | |
241 </conditional> | |
242 | |
243 <conditional name="etd_filtering"> | |
244 <param name="do_etd_filtering" type="select" label="ETD Filtering"> | |
245 <option value="none" selected="true">none</option> | |
246 <option value="default">yes (with default options)</option> | |
247 <option value="advanced">yes (show advanced options) </option> | |
248 </param> | |
249 <when value="none" /> | |
250 <when value="default" /> | |
251 <when value="advanced"> | |
252 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> | |
253 </param> | |
254 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> | |
255 <option value="MZ" selected="true">mz</option> | |
256 <option value="PPM">ppm</option> | |
257 </param> | |
258 <param name="remove_precursor" type="select" label="ETD Remove Precursor"> | |
259 <option value="true" selected="true">yes</option> | |
260 <option value="false">no</option> | |
261 </param> | |
262 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> | |
263 <option value="true" selected="true">yes</option> | |
264 <option value="false">no</option> | |
265 </param> | |
266 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> | |
267 <option value="true" selected="true">yes</option> | |
268 <option value="false">no</option> | |
269 </param> | |
270 <param name="blanket_removal" type="select" label="ETD Blanket Removal"> | |
271 <option value="true" selected="true">yes</option> | |
272 <option value="false">no</option> | |
273 </param> | |
274 </when> | |
275 </conditional> | |
276 | |
277 | |
278 <!-- BEGIN_VERSION_3 --> | |
279 <conditional name="ms2denoise"> | |
280 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" /> | |
281 <when value="true"> | |
282 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> | |
283 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> | |
284 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> | |
285 </when> | |
286 <when value="false" /> | |
287 </conditional> | |
288 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> | |
289 | |
290 <param name="polarity" type="select" label="Filter by Polarity"> | |
291 <option value="false" selected="true">no</option> | |
292 <option value="positive">positive</option> | |
293 <option value="negative">negative</option> | |
294 </param> | |
295 | |
296 <param name="analyzer" type="select" label="Filter by Analyzer"> | |
297 <option value="false" selected="true">no</option> | |
298 <option value="quad">quad</option> | |
299 <option value="orbi">orbi</option> | |
300 <option value="FT">FT</option> | |
301 <option value="IT">IT</option> | |
302 <option value="TOF">TOF</option> | |
303 </param> | |
304 <!-- END_VERSION_3 --> | |
305 </when> | |
306 </conditional> | |
307 | |
308 <conditional name="settings"> | |
309 <param name="settingsType" type="select" label="Advanced Settings" help=""> | |
310 <option value="default">Use Defaults</option> | |
311 <option value="full">Full Parameter List</option> | |
312 </param> | |
313 <when value="default" /> | |
314 <when value="full"> | |
315 <param type="select" name="binary_encoding" label="Binary Encoding Precision"> | |
316 <option value="64" selected="true">64</option> | |
317 <option value="32">32</option> | |
318 </param> | |
319 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> | |
320 <option value="64" selected="true">64</option> | |
321 <option value="32">32</option> | |
322 </param> | |
323 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> | |
324 <option value="64">64</option> | |
325 <option value="32" selected="true">32</option> | |
326 </param> | |
327 <param type="boolean" name="zlib" label="Use zlib"> | |
328 </param> | |
329 </when> | |
330 </conditional> | |
331 | |
332 | |
333 </inputs> | |
334 <outputs> | |
335 <data format="mzml" name="output"> | |
336 <change_format> | |
337 <when input="output_type" value="mzXML" format="mzxml" /> | |
338 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> | |
339 <when input="output_type" value="ms2" format="ms2" /> | |
340 <when input="output_type" value="mgf" format="mgf" /> | |
341 </change_format> | |
342 </data> | |
343 </outputs> | |
344 <help> | |
345 **What it does** | |
346 | |
347 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. | |
348 | |
349 You can view the original documentation here_. | |
350 | |
351 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | |
352 | |
353 ------ | |
354 | |
355 **Citation** | |
356 | |
357 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.` | |
358 | |
359 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert | |
360 | |
361 </help> | |
362 </tool> |