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comparison msconvert.xml.template @ 7:37e5502441cc draft

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author galaxyp
date Mon, 17 Feb 2014 17:00:29 -0500
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6:ffe1dca94595 7:37e5502441cc
1 <tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0">
2 <!-- BEGIN_VERSION_RAW -->
3 <description>Convert and filter a Thermo Finnigan RAW file</description>
4 <!-- END_VERSION_RAW -->
5 <!-- BEGIN_VERSION_DEFAULT -->
6 <description>Convert and filter a mass spec peak list</description>
7 <!-- END_VERSION_DEFAULT -->
8
9 <command interpreter="python">
10 #set $ext = $input.ext
11 #if $ext.startswith("m:")
12 #set $ext = $ext[len("m:"):]
13 #end if
14 msconvert_wrapper.py
15 --input=${input}
16 #if hasattr($input, 'display_name')
17 --input_name='${input.display_name}'
18 #end if
19 --output=${output}
20 ## BEGIN_VERSION_DEFAULT
21 --fromextension=$ext
22 ## END_VERSION_DEFAULT
23
24 ## BEGIN_VERSION_RAW
25 --fromextension=RAW
26 ## END_VERSION_RAW
27
28 --toextension=${output_type}
29
30 #if $settings.settingsType == "full"
31 --binaryencoding=${settings.binary_encoding}
32 --mzencoding=${settings.mz_encoding}
33 --intensityencoding=${settings.intensity_encoding}
34 --zlib=${settings.zlib}
35 #end if
36
37 #if $filtering.filtering_use
38
39 #if $filtering.precursor_recalculation.value
40 --filter "precursorRecalculation"
41 #end if
42
43 #if $filtering.peak_picking.pick_peaks
44 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
45 #end if
46
47 #if str($filtering.activation) != "false"
48 --filter "activation $filtering.activation"
49 #end if
50
51 #if len($filtering.indices) > 0
52 --filter "index
53 #for $index in $filtering.indices
54 [${index.from},${index.to}]
55 #end for
56 "
57 #end if
58
59 #if len($filtering.scan_numbers) > 0
60 --filter "scanNumber
61 #for $scan_number in $filtering.scan_numbers
62 [${scan_number.from},${scan_number.to}]
63 #end for
64 "
65 #end if
66
67 #for threshold_entry in $filtering.threshold_repeat
68 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
69 #end for
70
71
72 #if $filtering.strip_it.value
73 --filter "stripIT"
74 #end if
75
76 #if $filtering.filter_mz_windows.do_filter
77 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
78 #end if
79
80
81 #if $filtering.filter_ms_levels.do_filter
82 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
83 #end if
84
85 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
86 --filter "ETDFilter"
87 #end if
88
89 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
90 --filter "ETDFilter removePrecursor:$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"
91 #end if
92
93 ## BEGIN_VERSION_3
94
95 #if $filtering.precursor_refine.value
96 --filter "precursorRefine"
97 #end if
98
99 #if $filtering.ms2denoise.denoise
100 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
101 #end if
102
103 #if str($filtering.ms2deisotope) == "true"
104 --filter "MS2Deisotope"
105 #end if
106
107 #if str($filtering.polarity) != "false"
108 --filter "polarity $filtering.polarity"
109 #end if
110
111 #if str($filtering.analyzer) != "false"
112 --filter "analyzer $filtering.analyzer"
113 #end if
114
115 ## END_VERSION_3
116
117 #end if
118
119 </command>
120
121 <inputs>
122 <!-- BEGIN_VERSION_RAW -->
123 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
124 <!-- END_VERSION_RAW -->
125
126 <!-- BEGIN_VERSION_DEFAULT -->
127 <conditional name="type">
128 <param name="input_type" type="select" label="Input Type">
129 <option value="mzml">mzML</option>
130 <option value="mzxml">mzXML</option>
131 <option value="mgf">mgf</option>
132 <option value="ms2">ms2</option>
133 </param>
134 <when value="mzml">
135 <param format="mzml" name="input" type="data" label="Input mzML"/>
136 </when>
137 <when value="mzxml">
138 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
139 </when>
140 <when value="mgf">
141 <param format="mgf" name="input" type="data" label="Input mgf"/>
142 </when>
143 <when value="ms2">
144 <param format="ms2" name="input" type="data" label="Input ms2"/>
145 </when>
146 </conditional>
147 <!-- END_VERSION_DEFAULT -->
148 <param name="output_type" type="select" label="Output Type">
149 <option value="mzML">mzML (indexed)</option>
150 <option value="unindexed_mzML">mzML (unindexed)</option>
151 <option value="mzXML">mzXML (indexed)</option>
152 <option value="unindexed_mzXML">mzXML (unindexed)</option>
153 <option value="mgf">mgf</option>
154 <option value="ms2">ms2</option>
155 </param>
156 <conditional name="filtering">
157 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
158 <when value="false" />
159 <when value="true">
160 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
161 <!-- BEGIN_VERSION_3 -->
162 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
163 <!-- END_VERSION_3 -->
164
165
166 <conditional name="peak_picking">
167 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
168 <when value="false" />
169 <when value="true">
170 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
171 <option value="1">MS1 Only (1)</option>
172 <option value="2">MS2 Only (2)</option>
173 <option value="2-">MS2 and on (2-)</option>
174 <option value="1-">All Levels (1-)</option>
175 </param>
176 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
177 </when>
178 </conditional>
179
180 <repeat name="threshold_repeat" title="Filter by Threshold">
181 <conditional name="threshold">
182 <param type="select" label="Specify threshold on" name="threshold_type" help="">
183 <option value="count">Peak count</option>
184 <option value="count-after-ties">Peak count (after ties)</option>
185 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
186 <option value="bpi-relative">Percent of base peak intensity</option>
187 <option value="tic-relative">Percent of total ion current</option>
188 <option value="tic-fraction">Aggregate percent of total ion current</option>
189 </param>
190 <when value="count">
191 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
192 </when>
193 <when value="count-after-ties">
194 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
195 </when>
196 <when value="absolute">
197 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
198 </when>
199 <when value="bpi-relative">
200 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
201 />
202 </when>
203 <when value="tic-relative">
204 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
205 />
206 </when>
207 <when value="tic-fraction">
208 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
209 </when>
210 </conditional>
211 <param type="select" label="Keep" name="orientation">
212 <option value="most-intense">Most intense peaks</option>
213 <option value="least-intense">Least intense peaks</option>
214 </param>
215 </repeat>
216
217
218 <param name="activation" type="select" label="Filter by Activation">
219 <option value="false" selected="true">no</option>
220 <option value="ETD">ETD</option>
221 <option value="CID">CID</option>
222 <option value="SA">SA</option>
223 <option value="HCD">HCD</option>
224 <!-- BEGIN_VERSION_3 -->
225 <option>BIRD</option>
226 <option>ECD</option>
227 <option>IRMPD</option>
228 <option>PD</option>
229 <option>PSD</option>
230 <option>PQD</option>
231 <option>SID</option>
232 <option>SORI</option>
233 <!-- END_VERSION_3 -->
234 </param>
235
236 <repeat name="indices" title="Filter Scan Indices">
237 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
238 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
239 </repeat>
240
241 <repeat name="scan_numbers" title="Filter Scan Numbers">
242 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
243 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
244 </repeat>
245
246 <conditional name="filter_mz_windows">
247 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
248 <when value="false" />
249 <when value="true">
250 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
251 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
252 </when>
253 </conditional>
254
255 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
256
257 <conditional name="filter_ms_levels">
258 <param name="do_filter" type="boolean" label="Filter MS Levels" />
259 <when value="false" />
260 <when value="true">
261 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
262 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
263 </when>
264 </conditional>
265
266 <conditional name="etd_filtering">
267 <param name="do_etd_filtering" type="select" label="ETD Filtering">
268 <option value="none" selected="true">none</option>
269 <option value="default">yes (with default options)</option>
270 <option value="advanced">yes (show advanced options) </option>
271 </param>
272 <when value="none" />
273 <when value="default" />
274 <when value="advanced">
275 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
276 </param>
277 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
278 <option value="MZ" selected="true">mz</option>
279 <option value="PPM">ppm</option>
280 </param>
281 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
282 <option value="true" selected="true">yes</option>
283 <option value="false">no</option>
284 </param>
285 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
286 <option value="true" selected="true">yes</option>
287 <option value="false">no</option>
288 </param>
289 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
290 <option value="true" selected="true">yes</option>
291 <option value="false">no</option>
292 </param>
293 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
294 <option value="true" selected="true">yes</option>
295 <option value="false">no</option>
296 </param>
297 </when>
298 </conditional>
299
300
301 <!-- BEGIN_VERSION_3 -->
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 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
312
313 <param name="polarity" type="select" label="Filter by Polarity">
314 <option value="false" selected="true">no</option>
315 <option value="positive">positive</option>
316 <option value="negative">negative</option>
317 </param>
318
319 <param name="analyzer" type="select" label="Filter by Analyzer">
320 <option value="false" selected="true">no</option>
321 <option value="quad">quad</option>
322 <option value="orbi">orbi</option>
323 <option value="FT">FT</option>
324 <option value="IT">IT</option>
325 <option value="TOF">TOF</option>
326 </param>
327 <!-- END_VERSION_3 -->
328 </when>
329 </conditional>
330
331 <conditional name="settings">
332 <param name="settingsType" type="select" label="Advanced Settings" help="">
333 <option value="default">Use Defaults</option>
334 <option value="full">Full Parameter List</option>
335 </param>
336 <when value="default" />
337 <when value="full">
338 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
339 <option value="64" selected="true">64</option>
340 <option value="32">32</option>
341 </param>
342 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
343 <option value="64" selected="true">64</option>
344 <option value="32">32</option>
345 </param>
346 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
347 <option value="64">64</option>
348 <option value="32" selected="true">32</option>
349 </param>
350 <param type="boolean" name="zlib" label="Use zlib">
351 </param>
352 </when>
353 </conditional>
354
355
356 </inputs>
357 <outputs>
358 <data format="mzml" name="output">
359 <change_format>
360 <when input="output_type" value="mzXML" format="mzxml" />
361 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
362 <when input="output_type" value="ms2" format="ms2" />
363 <when input="output_type" value="mgf" format="mgf" />
364 </change_format>
365 </data>
366 </outputs>
367
368 <requirements>
369 <requirement type="package">proteowizard</requirement>
370 <!-- BEGIN_VERSION_RAW -->
371 <requirement type="platform">windows</requirement>
372 <!-- END_VERSION_RAW -->
373 </requirements>
374
375 <help>
376 **What it does**
377
378 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
379
380 You can view the original documentation here_.
381
382 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
383
384 ------
385
386 **Citation**
387
388 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.`
389
390 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
391
392 </help>
393 </tool>