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comparison msconvert3.xml @ 0:d44fecaf27a2 draft

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author iracooke
date Tue, 18 Mar 2014 19:08:54 -0400
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-1:000000000000 0:d44fecaf27a2
1 <tool id="msconvert3" name="msconvert3" version="0.2.1">
2 <!-- BEGIN_VERSION_DEFAULT -->
3 <description>Convert and filter a mass spec peak list</description>
4 <!-- END_VERSION_DEFAULT -->
5 <requirements>
6 <requirement type="package">proteowizard</requirement>
7 </requirements>
8 <command interpreter="python">
9 #set $ext = $input.ext
10 #if $ext.startswith("m:")
11 #set $ext = $ext[len("m:"):]
12 #end if
13 msconvert_wrapper.py
14 --input=${input}
15 #if hasattr($input, 'display_name')
16 --input_name='${input.display_name}'
17 #end if
18 --output=${output}
19 ## BEGIN_VERSION_DEFAULT
20 --fromextension=$ext
21 ## END_VERSION_DEFAULT
22
23
24 --toextension=${output_type}
25
26 #if $settings.settingsType == "full"
27 --binaryencoding=${settings.binary_encoding}
28 --mzencoding=${settings.mz_encoding}
29 --intensityencoding=${settings.intensity_encoding}
30 --zlib=${settings.zlib}
31 #end if
32
33 #if $filtering.filtering_use
34
35 #if $filtering.precursor_recalculation.value
36 --filter "precursorRecalculation"
37 #end if
38
39 #if $filtering.peak_picking.pick_peaks
40 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
41 #end if
42
43 #if str($filtering.activation) != "false"
44 --filter "activation $filtering.activation"
45 #end if
46
47 #if len($filtering.indices) > 0
48 --filter "index
49 #for $index in $filtering.indices
50 [${index.from},${index.to}]
51 #end for
52 "
53 #end if
54
55 #if len($filtering.scan_numbers) > 0
56 --filter "scanNumber
57 #for $scan_number in $filtering.scan_numbers
58 [${scan_number.from},${scan_number.to}]
59 #end for
60 "
61 #end if
62
63 #for threshold_entry in $filtering.threshold_repeat
64 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
65 #end for
66
67
68 #if $filtering.strip_it.value
69 --filter "stripIT"
70 #end if
71
72 #if $filtering.filter_mz_windows.do_filter
73 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
74 #end if
75
76
77 #if $filtering.filter_ms_levels.do_filter
78 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
79 #end if
80
81 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
82 --filter "ETDFilter"
83 #end if
84
85 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
86 --filter "ETDFilter removePrecursor:$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"
87 #end if
88
89 ## BEGIN_VERSION_3
90
91 #if $filtering.precursor_refine.value
92 --filter "precursorRefine"
93 #end if
94
95 #if $filtering.ms2denoise.denoise
96 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
97 #end if
98
99 #if str($filtering.ms2deisotope) == "true"
100 --filter "MS2Deisotope"
101 #end if
102
103 #if str($filtering.polarity) != "false"
104 --filter "polarity $filtering.polarity"
105 #end if
106
107 #if str($filtering.analyzer) != "false"
108 --filter "analyzer $filtering.analyzer"
109 #end if
110
111 ## END_VERSION_3
112
113 #end if
114
115 </command>
116
117 <inputs>
118
119 <!-- BEGIN_VERSION_DEFAULT -->
120 <conditional name="type">
121 <param name="input_type" type="select" label="Input Type">
122 <option value="mzml">mzML</option>
123 <option value="mzxml">mzXML</option>
124 <option value="mgf">mgf</option>
125 <option value="ms2">ms2</option>
126 </param>
127 <when value="mzml">
128 <param format="mzml" name="input" type="data" label="Input mzML"/>
129 </when>
130 <when value="mzxml">
131 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
132 </when>
133 <when value="mgf">
134 <param format="mgf" name="input" type="data" label="Input mgf"/>
135 </when>
136 <when value="ms2">
137 <param format="ms2" name="input" type="data" label="Input ms2"/>
138 </when>
139 </conditional>
140 <!-- END_VERSION_DEFAULT -->
141 <param name="output_type" type="select" label="Output Type">
142 <option value="mzML">mzML (indexed)</option>
143 <option value="unindexed_mzML">mzML (unindexed)</option>
144 <option value="mzXML">mzXML (indexed)</option>
145 <option value="unindexed_mzXML">mzXML (unindexed)</option>
146 <option value="mgf">mgf</option>
147 <option value="ms2">ms2</option>
148 </param>
149 <conditional name="filtering">
150 <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
151 <when value="false" />
152 <when value="true">
153 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
154 <!-- BEGIN_VERSION_3 -->
155 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
156 <!-- END_VERSION_3 -->
157
158
159 <conditional name="peak_picking">
160 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
161 <when value="false" />
162 <when value="true">
163 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
164 <option value="1">MS1 Only (1)</option>
165 <option value="2">MS2 Only (2)</option>
166 <option value="2-">MS2 and on (2-)</option>
167 <option value="1-">All Levels (1-)</option>
168 </param>
169 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
170 </when>
171 </conditional>
172
173 <repeat name="threshold_repeat" title="Filter by Threshold">
174 <conditional name="threshold">
175 <param type="select" label="Specify threshold on" name="threshold_type" help="">
176 <option value="count">Peak count</option>
177 <option value="count-after-ties">Peak count (after ties)</option>
178 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
179 <option value="bpi-relative">Percent of base peak intensity</option>
180 <option value="tic-relative">Percent of total ion current</option>
181 <option value="tic-fraction">Aggregate percent of total ion current</option>
182 </param>
183 <when value="count">
184 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
185 </when>
186 <when value="count-after-ties">
187 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
188 </when>
189 <when value="absolute">
190 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
191 </when>
192 <when value="bpi-relative">
193 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
194 />
195 </when>
196 <when value="tic-relative">
197 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
198 />
199 </when>
200 <when value="tic-fraction">
201 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
202 </when>
203 </conditional>
204 <param type="select" label="Keep" name="orientation">
205 <option value="most-intense">Most intense peaks</option>
206 <option value="least-intense">Least intense peaks</option>
207 </param>
208 </repeat>
209
210
211 <param name="activation" type="select" label="Filter by Activation">
212 <option value="false" selected="true">no</option>
213 <option value="ETD">ETD</option>
214 <option value="CID">CID</option>
215 <option value="SA">SA</option>
216 <option value="HCD">HCD</option>
217 <!-- BEGIN_VERSION_3 -->
218 <option>BIRD</option>
219 <option>ECD</option>
220 <option>IRMPD</option>
221 <option>PD</option>
222 <option>PSD</option>
223 <option>PQD</option>
224 <option>SID</option>
225 <option>SORI</option>
226 <!-- END_VERSION_3 -->
227 </param>
228
229 <repeat name="indices" title="Filter Scan Indices">
230 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
231 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
232 </repeat>
233
234 <repeat name="scan_numbers" title="Filter Scan Numbers">
235 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
236 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
237 </repeat>
238
239 <conditional name="filter_mz_windows">
240 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
241 <when value="false" />
242 <when value="true">
243 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
244 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
245 </when>
246 </conditional>
247
248 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
249
250 <conditional name="filter_ms_levels">
251 <param name="do_filter" type="boolean" label="Filter MS Levels" />
252 <when value="false" />
253 <when value="true">
254 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
255 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
256 </when>
257 </conditional>
258
259 <conditional name="etd_filtering">
260 <param name="do_etd_filtering" type="select" label="ETD Filtering">
261 <option value="none" selected="true">none</option>
262 <option value="default">yes (with default options)</option>
263 <option value="advanced">yes (show advanced options) </option>
264 </param>
265 <when value="none" />
266 <when value="default" />
267 <when value="advanced">
268 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
269 </param>
270 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
271 <option value="MZ" selected="true">mz</option>
272 <option value="PPM">ppm</option>
273 </param>
274 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
275 <option value="true" selected="true">yes</option>
276 <option value="false">no</option>
277 </param>
278 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
279 <option value="true" selected="true">yes</option>
280 <option value="false">no</option>
281 </param>
282 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
283 <option value="true" selected="true">yes</option>
284 <option value="false">no</option>
285 </param>
286 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
287 <option value="true" selected="true">yes</option>
288 <option value="false">no</option>
289 </param>
290 </when>
291 </conditional>
292
293
294 <!-- BEGIN_VERSION_3 -->
295 <conditional name="ms2denoise">
296 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
297 <when value="true">
298 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
299 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
300 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
301 </when>
302 <when value="false" />
303 </conditional>
304 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
305
306 <param name="polarity" type="select" label="Filter by Polarity">
307 <option value="false" selected="true">no</option>
308 <option value="positive">positive</option>
309 <option value="negative">negative</option>
310 </param>
311
312 <param name="analyzer" type="select" label="Filter by Analyzer">
313 <option value="false" selected="true">no</option>
314 <option value="quad">quad</option>
315 <option value="orbi">orbi</option>
316 <option value="FT">FT</option>
317 <option value="IT">IT</option>
318 <option value="TOF">TOF</option>
319 </param>
320 <!-- END_VERSION_3 -->
321 </when>
322 </conditional>
323
324 <conditional name="settings">
325 <param name="settingsType" type="select" label="Advanced Settings" help="">
326 <option value="default">Use Defaults</option>
327 <option value="full">Full Parameter List</option>
328 </param>
329 <when value="default" />
330 <when value="full">
331 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
332 <option value="64" selected="true">64</option>
333 <option value="32">32</option>
334 </param>
335 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
336 <option value="64" selected="true">64</option>
337 <option value="32">32</option>
338 </param>
339 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
340 <option value="64">64</option>
341 <option value="32" selected="true">32</option>
342 </param>
343 <param type="boolean" name="zlib" label="Use zlib">
344 </param>
345 </when>
346 </conditional>
347
348
349 </inputs>
350 <outputs>
351 <data format="mzml" name="output">
352 <change_format>
353 <when input="output_type" value="mzXML" format="mzxml" />
354 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
355 <when input="output_type" value="ms2" format="ms2" />
356 <when input="output_type" value="mgf" format="mgf" />
357 </change_format>
358 </data>
359 </outputs>
360 <help>
361 **What it does**
362
363 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
364
365 You can view the original documentation here_.
366
367 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
368
369 ------
370
371 **Citation**
372
373 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.`
374
375 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
376
377 </help>
378 </tool>