Mercurial > repos > galaxyp > msconvert
annotate msconvert_raw.xml @ 9:dd4ba10d0c45 draft
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author | galaxyp |
---|---|
date | Wed, 07 Dec 2016 16:43:07 -0500 |
parents | d2c61663e33c |
children |
rev | line source |
---|---|
8 | 1 <tool id="msconvert_raw" name="msconvert RAW" version="0.3.0"> |
2 <!-- BEGIN_VERSION_RAW --> | |
3 <description>Convert and filter a Thermo Finnigan RAW file</description> | |
4 <!-- END_VERSION_RAW --> | |
5 <requirements> | |
6 <!-- | |
7 <requirement type="package" version="3_0_4388">proteowizard</requirement> | |
8 --> | |
9 <!-- BEGIN_VERSION_RAW --> | |
10 <requirement type="platform">windows</requirement> | |
11 <!-- END_VERSION_RAW --> | |
12 </requirements> | |
13 <command interpreter="python"> | |
14 #set $ext = $input.ext | |
15 msconvert_wrapper.py | |
16 --input=${input} | |
17 #if hasattr($input, 'display_name') | |
18 --input_name='${input.display_name}' | |
19 #end if | |
20 --output=${output} | |
21 | |
22 ## BEGIN_VERSION_RAW | |
23 --fromextension=RAW | |
24 ## END_VERSION_RAW | |
25 | |
26 --toextension=${output_type} | |
27 | |
28 #if $settings.settingsType == "full" | |
29 --binaryencoding=${settings.binary_encoding} | |
30 --mzencoding=${settings.mz_encoding} | |
31 --intensityencoding=${settings.intensity_encoding} | |
32 --zlib=${settings.zlib} | |
33 #end if | |
34 | |
35 #if $filtering.filtering_use | |
36 | |
37 #if $filtering.precursor_recalculation.value | |
38 --filter "precursorRecalculation" | |
39 #end if | |
40 | |
41 #if $filtering.peak_picking.pick_peaks | |
42 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" | |
43 #end if | |
44 | |
45 #if str($filtering.activation) != "false" | |
46 --filter "activation $filtering.activation" | |
47 #end if | |
48 | |
49 #if len($filtering.indices) > 0 | |
50 --filter "index | |
51 #for $index in $filtering.indices | |
52 [${index.from},${index.to}] | |
53 #end for | |
54 " | |
55 #end if | |
56 | |
57 #if len($filtering.scan_numbers) > 0 | |
58 --filter "scanNumber | |
59 #for $scan_number in $filtering.scan_numbers | |
60 [${scan_number.from},${scan_number.to}] | |
61 #end for | |
62 " | |
63 #end if | |
64 | |
65 #for threshold_entry in $filtering.threshold_repeat | |
66 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" | |
67 #end for | |
68 | |
69 $filtering.strip_it | |
70 $filtering.metadataFixer | |
71 $filtering.sortByScanTime | |
72 | |
73 #if $filtering.filter_mz_windows.do_filter | |
74 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" | |
75 #end if | |
76 | |
77 #if $filtering.filter_chargeStatePredictor.do_filter | |
78 --filter "chargeStatePredictor $filtering.filter_chargeStatePredictor.overrideExistingCharge $filtering.filter_chargeStatePredictor.maxMultipleCharge $filtering.filter_chargeStatePredictor.minMultipleCharge $filtering.filter_chargeStatePredictor.singleChargeFractionTIC $filtering.filter_chargeStatePredictor.algorithmMakeMS2" | |
79 #end if | |
80 | |
81 | |
82 #if $filtering.filter_ms_levels.do_filter | |
83 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" | |
84 #end if | |
85 | |
86 #if str($filtering.etd_filtering.do_etd_filtering) == "default" | |
87 --filter "ETDFilter" | |
88 #end if | |
89 | |
90 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" | |
91 --filter "ETDFilter removePrecursor:$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" | |
92 #end if | |
93 | |
94 ## BEGIN_VERSION_3 | |
95 | |
96 #if $filtering.precursor_refine.value | |
97 --filter "precursorRefine" | |
98 #end if | |
99 | |
100 #if $filtering.ms2denoise.denoise | |
101 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax" | |
102 #end if | |
103 | |
104 #if str($filtering.ms2deisotope) == "true" | |
105 --filter "MS2Deisotope" | |
106 #end if | |
107 | |
108 #if str($filtering.polarity) != "false" | |
109 --filter "polarity $filtering.polarity" | |
110 #end if | |
111 | |
112 #if str($filtering.analyzer) != "false" | |
113 --filter "analyzer $filtering.analyzer" | |
114 #end if | |
115 | |
116 ## END_VERSION_3 | |
117 | |
118 #end if | |
119 | |
120 </command> | |
121 | |
122 <inputs> | |
123 <!-- BEGIN_VERSION_RAW --> | |
124 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> | |
125 <!-- END_VERSION_RAW --> | |
126 | |
127 <param name="output_type" type="select" label="Output Type"> | |
128 <option value="mzML">mzML (indexed)</option> | |
129 <option value="unindexed_mzML">mzML (unindexed)</option> | |
130 <option value="mzXML">mzXML (indexed)</option> | |
131 <option value="unindexed_mzXML">mzXML (unindexed)</option> | |
132 <option value="mgf">mgf</option> | |
133 <option value="ms2">ms2</option> | |
134 </param> | |
135 <conditional name="filtering"> | |
136 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> | |
137 <when value="false" /> | |
138 <when value="true"> | |
139 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> | |
140 <!-- BEGIN_VERSION_3 --> | |
141 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> | |
142 <!-- END_VERSION_3 --> | |
143 | |
144 | |
145 <conditional name="peak_picking"> | |
146 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> | |
147 <when value="false" /> | |
148 <when value="true"> | |
149 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> | |
150 <option value="1">MS1 Only (1)</option> | |
151 <option value="2">MS2 Only (2)</option> | |
152 <option value="2-">MS2 and on (2-)</option> | |
153 <option value="1-">All Levels (1-)</option> | |
154 </param> | |
155 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> | |
156 </when> | |
157 </conditional> | |
158 | |
159 <repeat name="threshold_repeat" title="Filter by Threshold"> | |
160 <conditional name="threshold"> | |
161 <param type="select" label="Specify threshold on" name="threshold_type" help=""> | |
162 <option value="count">Peak count</option> | |
163 <option value="count-after-ties">Peak count (after ties)</option> | |
164 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> | |
165 <option value="bpi-relative">Percent of base peak intensity</option> | |
166 <option value="tic-relative">Percent of total ion current</option> | |
167 <option value="tic-fraction">Aggregate percent of total ion current</option> | |
168 </param> | |
169 <when value="count"> | |
170 <param type="integer" name="value" label="Number of peaks to keep" value="100" /> | |
171 </when> | |
172 <when value="count-after-ties"> | |
173 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> | |
174 </when> | |
175 <when value="absolute"> | |
176 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> | |
177 </when> | |
178 <when value="bpi-relative"> | |
179 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" | |
180 /> | |
181 </when> | |
182 <when value="tic-relative"> | |
183 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" | |
184 /> | |
185 </when> | |
186 <when value="tic-fraction"> | |
187 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> | |
188 </when> | |
189 </conditional> | |
190 <param type="select" label="Keep" name="orientation"> | |
191 <option value="most-intense">Most intense peaks</option> | |
192 <option value="least-intense">Least intense peaks</option> | |
193 </param> | |
194 </repeat> | |
195 | |
196 <param name="activation" type="select" label="Filter by Activation"> | |
197 <option value="false" selected="true">no</option> | |
198 <option value="ETD">ETD</option> | |
199 <option value="CID">CID</option> | |
200 <option value="SA">SA</option> | |
201 <option value="HCD">HCD</option> | |
202 <!-- BEGIN_VERSION_3 --> | |
203 <option>BIRD</option> | |
204 <option>ECD</option> | |
205 <option>IRMPD</option> | |
206 <option>PD</option> | |
207 <option>PSD</option> | |
208 <option>PQD</option> | |
209 <option>SID</option> | |
210 <option>SORI</option> | |
211 <!-- END_VERSION_3 --> | |
212 </param> | |
213 | |
214 <repeat name="indices" title="Filter Scan Indices"> | |
215 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> | |
216 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> | |
217 </repeat> | |
218 | |
219 <repeat name="scan_numbers" title="Filter Scan Numbers"> | |
220 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> | |
221 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> | |
222 </repeat> | |
223 | |
224 <conditional name="filter_mz_windows"> | |
225 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> | |
226 <when value="false" /> | |
227 <when value="true"> | |
228 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> | |
229 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> | |
230 </when> | |
231 </conditional> | |
232 | |
233 <param name="strip_it" type="boolean" | |
234 truevalue="--filter 'stripIT'" falsevalue="" | |
235 label="Strip Ion Trap MS1 Scans" /> | |
236 <param name="metadataFixer" type="boolean" truevalue="--filter 'metadataFixer'" falsevalue="" | |
237 label="This filter is used to add or replace a spectra's TIC/BPI metadata" | |
238 help="It is usually used after peakPicking where the change from profile to centroided data may make the TIC and BPI values inconsistent with the revised scan data." /> | |
239 <param name="sortByScanTime" type="boolean" | |
240 truevalue="--filter 'sortByScanTime'" falsevalue="" | |
241 label=" This filter reorders spectra, sorting them by ascending scan start time." /> | |
242 | |
243 <conditional name="filter_chargeStatePredictor"> | |
244 <param name="do_filter" type="boolean" | |
245 label=" Predicts MSn spectrum precursors to be singly or multiply charged depending on the ratio of intensity above and below the precursor m/z" | |
246 help="or optionally using the 'makeMS2' algorithm" /> | |
247 <when value="false" /> | |
248 <when value="true"> | |
249 <param name="overrideExistingCharge" type="boolean" checked="True" truevalue="true" falsevalue="false" | |
250 label="always override existing charge information"/> | |
251 <param name="minMultipleCharge" type="integer" value="2" optional="true" | |
252 label="Minimum of the range of values to add to the spectrum's existing 'MS_possible_charge_state' values." | |
253 help="If these are the same values, the spectrum's MS_possible_charge_state values are removed and replaced with this single."/> | |
254 <param name="maxMultipleCharge" type="integer" value="3" optional="false" | |
255 label="Maximum of the range of values to add to the spectrum's existing 'MS_possible_charge_state' values." /> | |
256 | |
257 <param name="singleChargeFractionTIC" type="float" min="0.0" max="1.0" value="0.9" | |
258 help="Is a percentage expressed as a value between 0 and 1" | |
259 label="This is the value used as the previously mentioned ratio of intensity above and below the precursor m/z." /> | |
260 | |
261 <param name="algorithmMakeMS2" type="boolean" checked="False" truevalue="true" falsevalue="false" | |
262 label="Use 'makeMS2' algorithm instead of the one described above"/> | |
263 | |
264 </when> | |
265 <when value="false"/> | |
266 </conditional> | |
267 | |
268 <conditional name="filter_ms_levels"> | |
269 <param name="do_filter" type="boolean" label="Filter MS Levels" /> | |
270 <when value="false" /> | |
271 <when value="true"> | |
272 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> | |
273 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> | |
274 </when> | |
275 </conditional> | |
276 | |
277 <conditional name="etd_filtering"> | |
278 <param name="do_etd_filtering" type="select" label="ETD Filtering"> | |
279 <option value="none" selected="true">none</option> | |
280 <option value="default">yes (with default options)</option> | |
281 <option value="advanced">yes (show advanced options) </option> | |
282 </param> | |
283 <when value="none" /> | |
284 <when value="default" /> | |
285 <when value="advanced"> | |
286 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> | |
287 </param> | |
288 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> | |
289 <option value="MZ" selected="true">mz</option> | |
290 <option value="PPM">ppm</option> | |
291 </param> | |
292 <param name="remove_precursor" type="select" label="ETD Remove Precursor"> | |
293 <option value="true" selected="true">yes</option> | |
294 <option value="false">no</option> | |
295 </param> | |
296 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> | |
297 <option value="true" selected="true">yes</option> | |
298 <option value="false">no</option> | |
299 </param> | |
300 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> | |
301 <option value="true" selected="true">yes</option> | |
302 <option value="false">no</option> | |
303 </param> | |
304 <param name="blanket_removal" type="select" label="ETD Blanket Removal"> | |
305 <option value="true" selected="true">yes</option> | |
306 <option value="false">no</option> | |
307 </param> | |
308 </when> | |
309 </conditional> | |
310 | |
311 | |
312 <!-- BEGIN_VERSION_3 --> | |
313 <conditional name="ms2denoise"> | |
314 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" /> | |
315 <when value="true"> | |
316 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> | |
317 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> | |
318 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> | |
319 </when> | |
320 <when value="false" /> | |
321 </conditional> | |
322 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> | |
323 | |
324 <param name="polarity" type="select" label="Filter by Polarity"> | |
325 <option value="false" selected="true">no</option> | |
326 <option value="positive">positive</option> | |
327 <option value="negative">negative</option> | |
328 </param> | |
329 | |
330 <param name="analyzer" type="select" label="Filter by Analyzer"> | |
331 <option value="false" selected="true">no</option> | |
332 <option value="quad">quad</option> | |
333 <option value="orbi">orbi</option> | |
334 <option value="FT">FT</option> | |
335 <option value="IT">IT</option> | |
336 <option value="TOF">TOF</option> | |
337 </param> | |
338 <!-- END_VERSION_3 --> | |
339 </when> | |
340 </conditional> | |
341 | |
342 <conditional name="settings"> | |
343 <param name="settingsType" type="select" label="Advanced Settings" help=""> | |
344 <option value="default">Use Defaults</option> | |
345 <option value="full">Full Parameter List</option> | |
346 </param> | |
347 <when value="default" /> | |
348 <when value="full"> | |
349 <param type="select" name="binary_encoding" label="Binary Encoding Precision"> | |
350 <option value="64" selected="true">64</option> | |
351 <option value="32">32</option> | |
352 </param> | |
353 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> | |
354 <option value="64" selected="true">64</option> | |
355 <option value="32">32</option> | |
356 </param> | |
357 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> | |
358 <option value="64">64</option> | |
359 <option value="32" selected="true">32</option> | |
360 </param> | |
361 <param type="boolean" name="zlib" label="Use zlib"> | |
362 </param> | |
363 </when> | |
364 </conditional> | |
365 | |
366 | |
367 </inputs> | |
368 <outputs> | |
9
dd4ba10d0c45
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
8
diff
changeset
|
369 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" > |
8 | 370 <change_format> |
371 <when input="output_type" value="mzXML" format="mzxml" /> | |
372 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> | |
373 <when input="output_type" value="ms2" format="ms2" /> | |
374 <when input="output_type" value="mgf" format="mgf" /> | |
375 </change_format> | |
376 </data> | |
377 </outputs> | |
378 <help> | |
379 **What it does** | |
380 | |
381 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. | |
382 | |
383 You can view the original documentation here_. | |
384 | |
385 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | |
386 | |
387 ------ | |
388 | |
389 **Citation** | |
390 | |
391 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.` | |
392 | |
393 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert | |
394 | |
395 </help> | |
396 </tool> |