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comparison msconvert.xml @ 8:d2c61663e33c draft

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author galaxyp
date Fri, 26 Sep 2014 14:44:54 -0400
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7:37e5502441cc 8:d2c61663e33c
1 <tool id="msconvert" name="msconvert" version="0.3.0">
2 <!-- BEGIN_VERSION_DEFAULT -->
3 <description>Convert and filter a mass spec peak list</description>
4 <!-- END_VERSION_DEFAULT -->
5 <!--
6 <requirements>
7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
8 </requirements>
9 -->
10 <command interpreter="python">
11 #set $ext = $input.ext
12 msconvert_wrapper.py
13 --input=${input}
14 #if hasattr($input, 'display_name')
15 --input_name='${input.display_name}'
16 #end if
17 --output=${output}
18 ## BEGIN_VERSION_DEFAULT
19 --fromextension=$ext
20 ## END_VERSION_DEFAULT
21
22
23 --toextension=${output_type}
24
25 #if $settings.settingsType == "full"
26 --binaryencoding=${settings.binary_encoding}
27 --mzencoding=${settings.mz_encoding}
28 --intensityencoding=${settings.intensity_encoding}
29 --zlib=${settings.zlib}
30 #end if
31
32 #if $filtering.filtering_use
33
34 #if $filtering.precursor_recalculation.value
35 --filter "precursorRecalculation"
36 #end if
37
38 #if $filtering.peak_picking.pick_peaks
39 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
40 #end if
41
42 #if str($filtering.activation) != "false"
43 --filter "activation $filtering.activation"
44 #end if
45
46 #if len($filtering.indices) > 0
47 --filter "index
48 #for $index in $filtering.indices
49 [${index.from},${index.to}]
50 #end for
51 "
52 #end if
53
54 #if len($filtering.scan_numbers) > 0
55 --filter "scanNumber
56 #for $scan_number in $filtering.scan_numbers
57 [${scan_number.from},${scan_number.to}]
58 #end for
59 "
60 #end if
61
62 #for threshold_entry in $filtering.threshold_repeat
63 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
64 #end for
65
66
67 #if $filtering.strip_it.value
68 --filter "stripIT"
69 #end if
70
71 #if $filtering.filter_mz_windows.do_filter
72 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
73 #end if
74
75
76 #if $filtering.filter_ms_levels.do_filter
77 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
78 #end if
79
80 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
81 --filter "ETDFilter"
82 #end if
83
84 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
85 --filter "ETDFilter removePrecursor:$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"
86 #end if
87
88 ## BEGIN_VERSION_3
89
90 #if $filtering.precursor_refine.value
91 --filter "precursorRefine"
92 #end if
93
94 #if $filtering.ms2denoise.denoise
95 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
96 #end if
97
98 #if str($filtering.ms2deisotope) == "true"
99 --filter "MS2Deisotope"
100 #end if
101
102 #if str($filtering.polarity) != "false"
103 --filter "polarity $filtering.polarity"
104 #end if
105
106 #if str($filtering.analyzer) != "false"
107 --filter "analyzer $filtering.analyzer"
108 #end if
109
110 ## END_VERSION_3
111
112 #end if
113
114 </command>
115
116 <inputs>
117
118 <!-- BEGIN_VERSION_DEFAULT -->
119 <conditional name="type">
120 <param name="input_type" type="select" label="Input Type">
121 <option value="mzml">mzML</option>
122 <option value="mzxml">mzXML</option>
123 <option value="mgf">mgf</option>
124 <option value="ms2">ms2</option>
125 </param>
126 <when value="mzml">
127 <param format="mzml" name="input" type="data" label="Input mzML"/>
128 </when>
129 <when value="mzxml">
130 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
131 </when>
132 <when value="mgf">
133 <param format="mgf" name="input" type="data" label="Input mgf"/>
134 </when>
135 <when value="ms2">
136 <param format="ms2" name="input" type="data" label="Input ms2"/>
137 </when>
138 </conditional>
139 <!-- END_VERSION_DEFAULT -->
140 <param name="output_type" type="select" label="Output Type">
141 <option value="mzML">mzML (indexed)</option>
142 <option value="unindexed_mzML">mzML (unindexed)</option>
143 <option value="mzXML">mzXML (indexed)</option>
144 <option value="unindexed_mzXML">mzXML (unindexed)</option>
145 <option value="mgf">mgf</option>
146 <option value="ms2">ms2</option>
147 </param>
148 <conditional name="filtering">
149 <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
150 <when value="false" />
151 <when value="true">
152 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
153 <!-- BEGIN_VERSION_3 -->
154 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
155 <!-- END_VERSION_3 -->
156
157
158 <conditional name="peak_picking">
159 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
160 <when value="false" />
161 <when value="true">
162 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
163 <option value="1">MS1 Only (1)</option>
164 <option value="2">MS2 Only (2)</option>
165 <option value="2-">MS2 and on (2-)</option>
166 <option value="1-">All Levels (1-)</option>
167 </param>
168 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
169 </when>
170 </conditional>
171
172 <repeat name="threshold_repeat" title="Filter by Threshold">
173 <conditional name="threshold">
174 <param type="select" label="Specify threshold on" name="threshold_type" help="">
175 <option value="count">Peak count</option>
176 <option value="count-after-ties">Peak count (after ties)</option>
177 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
178 <option value="bpi-relative">Percent of base peak intensity</option>
179 <option value="tic-relative">Percent of total ion current</option>
180 <option value="tic-fraction">Aggregate percent of total ion current</option>
181 </param>
182 <when value="count">
183 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
184 </when>
185 <when value="count-after-ties">
186 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
187 </when>
188 <when value="absolute">
189 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
190 </when>
191 <when value="bpi-relative">
192 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
193 />
194 </when>
195 <when value="tic-relative">
196 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
197 />
198 </when>
199 <when value="tic-fraction">
200 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
201 </when>
202 </conditional>
203 <param type="select" label="Keep" name="orientation">
204 <option value="most-intense">Most intense peaks</option>
205 <option value="least-intense">Least intense peaks</option>
206 </param>
207 </repeat>
208
209
210 <param name="activation" type="select" label="Filter by Activation">
211 <option value="false" selected="true">no</option>
212 <option value="ETD">ETD</option>
213 <option value="CID">CID</option>
214 <option value="SA">SA</option>
215 <option value="HCD">HCD</option>
216 <!-- BEGIN_VERSION_3 -->
217 <option>BIRD</option>
218 <option>ECD</option>
219 <option>IRMPD</option>
220 <option>PD</option>
221 <option>PSD</option>
222 <option>PQD</option>
223 <option>SID</option>
224 <option>SORI</option>
225 <!-- END_VERSION_3 -->
226 </param>
227
228 <repeat name="indices" title="Filter Scan Indices">
229 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
230 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
231 </repeat>
232
233 <repeat name="scan_numbers" title="Filter Scan Numbers">
234 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
235 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
236 </repeat>
237
238 <conditional name="filter_mz_windows">
239 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
240 <when value="false" />
241 <when value="true">
242 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
243 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
244 </when>
245 </conditional>
246
247 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
248
249 <conditional name="filter_ms_levels">
250 <param name="do_filter" type="boolean" label="Filter MS Levels" />
251 <when value="false" />
252 <when value="true">
253 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
254 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
255 </when>
256 </conditional>
257
258 <conditional name="etd_filtering">
259 <param name="do_etd_filtering" type="select" label="ETD Filtering">
260 <option value="none" selected="true">none</option>
261 <option value="default">yes (with default options)</option>
262 <option value="advanced">yes (show advanced options) </option>
263 </param>
264 <when value="none" />
265 <when value="default" />
266 <when value="advanced">
267 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
268 </param>
269 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
270 <option value="MZ" selected="true">mz</option>
271 <option value="PPM">ppm</option>
272 </param>
273 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
274 <option value="true" selected="true">yes</option>
275 <option value="false">no</option>
276 </param>
277 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
278 <option value="true" selected="true">yes</option>
279 <option value="false">no</option>
280 </param>
281 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
282 <option value="true" selected="true">yes</option>
283 <option value="false">no</option>
284 </param>
285 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
286 <option value="true" selected="true">yes</option>
287 <option value="false">no</option>
288 </param>
289 </when>
290 </conditional>
291
292
293 <!-- BEGIN_VERSION_3 -->
294 <conditional name="ms2denoise">
295 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
296 <when value="true">
297 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
298 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
299 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
300 </when>
301 <when value="false" />
302 </conditional>
303 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
304
305 <param name="polarity" type="select" label="Filter by Polarity">
306 <option value="false" selected="true">no</option>
307 <option value="positive">positive</option>
308 <option value="negative">negative</option>
309 </param>
310
311 <param name="analyzer" type="select" label="Filter by Analyzer">
312 <option value="false" selected="true">no</option>
313 <option value="quad">quad</option>
314 <option value="orbi">orbi</option>
315 <option value="FT">FT</option>
316 <option value="IT">IT</option>
317 <option value="TOF">TOF</option>
318 </param>
319 <!-- END_VERSION_3 -->
320 </when>
321 </conditional>
322
323 <conditional name="settings">
324 <param name="settingsType" type="select" label="Advanced Settings" help="">
325 <option value="default">Use Defaults</option>
326 <option value="full">Full Parameter List</option>
327 </param>
328 <when value="default" />
329 <when value="full">
330 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
331 <option value="64" selected="true">64</option>
332 <option value="32">32</option>
333 </param>
334 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
335 <option value="64" selected="true">64</option>
336 <option value="32">32</option>
337 </param>
338 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
339 <option value="64">64</option>
340 <option value="32" selected="true">32</option>
341 </param>
342 <param type="boolean" name="zlib" label="Use zlib">
343 </param>
344 </when>
345 </conditional>
346
347
348 </inputs>
349 <outputs>
350 <data format="mzml" name="output">
351 <change_format>
352 <when input="output_type" value="mzXML" format="mzxml" />
353 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
354 <when input="output_type" value="ms2" format="ms2" />
355 <when input="output_type" value="mgf" format="mgf" />
356 </change_format>
357 </data>
358 </outputs>
359 <help>
360 **What it does**
361
362 Allows interconversion within various mass spectrometry peak list formats. 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/msconvert
375
376 </help>
377 </tool>