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comparison msconvert.xml @ 7:e638f7fad66a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:21:27 -0500
parents 6b6bba73eadb
children 06747cba5685
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6:6b6bba73eadb 7:e638f7fad66a
1 <tool id="msconvert" name="msconvert" version="0.3.0"> 1 <tool id="msconvert" name="msconvert" version="@VERSION@.0">
2 <!-- BEGIN_VERSION_DEFAULT --> 2 <description>Convert and/or filter mass spectrometry files</description>
3 <description>Convert and filter a mass spec peak list</description> 3 <macros>
4 <!-- END_VERSION_DEFAULT --> 4 <import>msconvert_macros.xml</import>
5 <!-- 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3_0_4388">proteowizard</requirement> 7 <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
8 </requirements> 8 </requirements>
9 --> 9 <expand macro="msconvertCommand" />
10 <command interpreter="python"> 10 <inputs>
11 #import re 11 <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
12 #set $ext = $input.ext 12 <expand macro="msconvertInputParameters" />
13 msconvert_wrapper.py
14 #if $type.input_type == 'wiff':
15 #set basename = 'absciex'
16 #if hasattr($input, 'display_name')
17 #set basename = $re.sub('\W','_',$input.display_name)
18 #end if
19 --input=${input.extra_files_path}/wiff
20 --input_name='${basename}.wiff
21 --implicit=${input.extra_files_path}/wiff_scan
22 --input=${input.extra_files_path}/wiff_scan
23 --input_name='${basename}.wiff.scan
24 #else
25 --input=${input}
26 #if hasattr($input, 'display_name')
27 --input_name='${input.display_name}'
28 #end if
29 #end if
30 --output=${output}
31 ## BEGIN_VERSION_DEFAULT
32 --fromextension=$ext
33 ## END_VERSION_DEFAULT
34
35
36 --toextension=${output_type}
37
38 #if $settings.settingsType == "full"
39 --binaryencoding=${settings.binary_encoding}
40 --mzencoding=${settings.mz_encoding}
41 --intensityencoding=${settings.intensity_encoding}
42 --zlib=${settings.zlib}
43 #end if
44
45 #if $filtering.filtering_use
46
47 #if $filtering.precursor_recalculation.value
48 --filter "precursorRecalculation"
49 #end if
50
51 #if $filtering.peak_picking.pick_peaks
52 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
53 #end if
54
55 #if str($filtering.activation) != "false"
56 --filter "activation $filtering.activation"
57 #end if
58
59 #if len($filtering.indices) > 0
60 --filter "index
61 #for $index in $filtering.indices
62 [${index.from},${index.to}]
63 #end for
64 "
65 #end if
66
67 #if len($filtering.scan_numbers) > 0
68 --filter "scanNumber
69 #for $scan_number in $filtering.scan_numbers
70 [${scan_number.from},${scan_number.to}]
71 #end for
72 "
73 #end if
74
75 #for threshold_entry in $filtering.threshold_repeat
76 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
77 #end for
78
79
80 #if $filtering.strip_it.value
81 --filter "stripIT"
82 #end if
83
84 #if $filtering.filter_mz_windows.do_filter
85 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
86 #end if
87
88
89 #if $filtering.filter_ms_levels.do_filter
90 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
91 #end if
92
93 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
94 --filter "ETDFilter"
95 #end if
96
97 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
98 --filter "ETDFilter removePrecursor:$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"
99 #end if
100
101 ## BEGIN_VERSION_3
102
103 #if $filtering.precursor_refine.value
104 --filter "precursorRefine"
105 #end if
106
107 #if $filtering.ms2denoise.denoise
108 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
109 #end if
110
111 #if str($filtering.ms2deisotope) == "true"
112 --filter "MS2Deisotope"
113 #end if
114
115 #if str($filtering.polarity) != "false"
116 --filter "polarity $filtering.polarity"
117 #end if
118
119 #if str($filtering.analyzer) != "false"
120 --filter "analyzer $filtering.analyzer"
121 #end if
122
123 ## END_VERSION_3
124
125 #end if
126
127 </command>
128
129 <inputs>
130
131 <!-- BEGIN_VERSION_DEFAULT -->
132 <conditional name="type">
133 <param name="input_type" type="select" label="Input Type">
134 <option value="mzml">mzML</option>
135 <option value="mzxml">mzXML</option>
136 <option value="mgf">mgf</option>
137 <option value="ms2">ms2</option>
138 <option value="wiff">wiff</option>
139 </param>
140 <when value="mzml">
141 <param format="mzml" name="input" type="data" label="Input mzML"/>
142 </when>
143 <when value="mzxml">
144 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
145 </when>
146 <when value="mgf">
147 <param format="mgf" name="input" type="data" label="Input mgf"/>
148 </when>
149 <when value="ms2">
150 <param format="ms2" name="input" type="data" label="Input ms2"/>
151 </when>
152 <when value="wiff">
153 <param format="wiff" name="input" type="data" label="Input wiff"/>
154 </when>
155 </conditional>
156 <!-- END_VERSION_DEFAULT -->
157 <param name="output_type" type="select" label="Output Type">
158 <option value="mzML">mzML (indexed)</option>
159 <option value="unindexed_mzML">mzML (unindexed)</option>
160 <option value="mzXML">mzXML (indexed)</option>
161 <option value="unindexed_mzXML">mzXML (unindexed)</option>
162 <option value="mgf">mgf</option>
163 <option value="ms2">ms2</option>
164 </param>
165 <conditional name="filtering">
166 <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
167 <when value="false" />
168 <when value="true">
169 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
170 <!-- BEGIN_VERSION_3 -->
171 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
172 <!-- END_VERSION_3 -->
173
174
175 <conditional name="peak_picking">
176 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
177 <when value="false" />
178 <when value="true">
179 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
180 <option value="1">MS1 Only (1)</option>
181 <option value="2">MS2 Only (2)</option>
182 <option value="2-">MS2 and on (2-)</option>
183 <option value="1-">All Levels (1-)</option>
184 </param>
185 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
186 </when>
187 </conditional>
188
189 <repeat name="threshold_repeat" title="Filter by Threshold">
190 <conditional name="threshold">
191 <param type="select" label="Specify threshold on" name="threshold_type" help="">
192 <option value="count">Peak count</option>
193 <option value="count-after-ties">Peak count (after ties)</option>
194 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
195 <option value="bpi-relative">Percent of base peak intensity</option>
196 <option value="tic-relative">Percent of total ion current</option>
197 <option value="tic-fraction">Aggregate percent of total ion current</option>
198 </param>
199 <when value="count">
200 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
201 </when>
202 <when value="count-after-ties">
203 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
204 </when>
205 <when value="absolute">
206 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
207 </when>
208 <when value="bpi-relative">
209 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
210 />
211 </when>
212 <when value="tic-relative">
213 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
214 />
215 </when>
216 <when value="tic-fraction">
217 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
218 </when>
219 </conditional>
220 <param type="select" label="Keep" name="orientation">
221 <option value="most-intense">Most intense peaks</option>
222 <option value="least-intense">Least intense peaks</option>
223 </param>
224 </repeat>
225
226
227 <param name="activation" type="select" label="Filter by Activation">
228 <option value="false" selected="true">no</option>
229 <option value="ETD">ETD</option>
230 <option value="CID">CID</option>
231 <option value="SA">SA</option>
232 <option value="HCD">HCD</option>
233 <!-- BEGIN_VERSION_3 -->
234 <option>BIRD</option>
235 <option>ECD</option>
236 <option>IRMPD</option>
237 <option>PD</option>
238 <option>PSD</option>
239 <option>PQD</option>
240 <option>SID</option>
241 <option>SORI</option>
242 <!-- END_VERSION_3 -->
243 </param>
244
245 <repeat name="indices" title="Filter Scan Indices">
246 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
247 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
248 </repeat>
249
250 <repeat name="scan_numbers" title="Filter Scan Numbers">
251 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
252 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
253 </repeat>
254
255 <conditional name="filter_mz_windows">
256 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
257 <when value="false" />
258 <when value="true">
259 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
260 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
261 </when>
262 </conditional>
263
264 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
265
266 <conditional name="filter_ms_levels">
267 <param name="do_filter" type="boolean" label="Filter MS Levels" />
268 <when value="false" />
269 <when value="true">
270 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
271 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
272 </when>
273 </conditional>
274
275 <conditional name="etd_filtering">
276 <param name="do_etd_filtering" type="select" label="ETD Filtering">
277 <option value="none" selected="true">none</option>
278 <option value="default">yes (with default options)</option>
279 <option value="advanced">yes (show advanced options) </option>
280 </param>
281 <when value="none" />
282 <when value="default" />
283 <when value="advanced">
284 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
285 </param>
286 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
287 <option value="MZ" selected="true">mz</option>
288 <option value="PPM">ppm</option>
289 </param>
290 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
291 <option value="true" selected="true">yes</option>
292 <option value="false">no</option>
293 </param>
294 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
295 <option value="true" selected="true">yes</option>
296 <option value="false">no</option>
297 </param>
298 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
299 <option value="true" selected="true">yes</option>
300 <option value="false">no</option>
301 </param>
302 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
303 <option value="true" selected="true">yes</option>
304 <option value="false">no</option>
305 </param>
306 </when>
307 </conditional>
308
309
310 <!-- BEGIN_VERSION_3 -->
311 <conditional name="ms2denoise">
312 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
313 <when value="true">
314 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
315 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
316 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
317 </when>
318 <when value="false" />
319 </conditional>
320 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
321
322 <param name="polarity" type="select" label="Filter by Polarity">
323 <option value="false" selected="true">no</option>
324 <option value="positive">positive</option>
325 <option value="negative">negative</option>
326 </param>
327
328 <param name="analyzer" type="select" label="Filter by Analyzer">
329 <option value="false" selected="true">no</option>
330 <option value="quad">quad</option>
331 <option value="orbi">orbi</option>
332 <option value="FT">FT</option>
333 <option value="IT">IT</option>
334 <option value="TOF">TOF</option>
335 </param>
336 <!-- END_VERSION_3 -->
337 </when>
338 </conditional>
339
340 <conditional name="settings">
341 <param name="settingsType" type="select" label="Advanced Settings" help="">
342 <option value="default">Use Defaults</option>
343 <option value="full">Full Parameter List</option>
344 </param>
345 <when value="default" />
346 <when value="full">
347 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
348 <option value="64" selected="true">64</option>
349 <option value="32">32</option>
350 </param>
351 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
352 <option value="64" selected="true">64</option>
353 <option value="32">32</option>
354 </param>
355 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
356 <option value="64">64</option>
357 <option value="32" selected="true">32</option>
358 </param>
359 <param type="boolean" name="zlib" label="Use zlib">
360 </param>
361 </when>
362 </conditional>
363
364
365 </inputs> 13 </inputs>
366 <outputs> 14 <expand macro="msconvertOutput" />
367 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > 15 <tests>
368 <change_format> 16 <expand macro="msconvert_tests" />
369 <when input="output_type" value="mzXML" format="mzxml" /> 17 </tests>
370 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
371 <when input="output_type" value="ms2" format="ms2" />
372 <when input="output_type" value="mgf" format="mgf" />
373 </change_format>
374 </data>
375 </outputs>
376 <help> 18 <help>
377 **What it does** 19 <expand macro="msconvert_help" />
378
379 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
380
381 You can view the original documentation here_.
382
383 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
384
385 ------
386
387 **Citation**
388
389 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.`
390
391 If you use this tool in Galaxy, please cite Chilton J, et al.
392 https://github.com/galaxyproteomics/tools-galaxyp/
393
394 </help> 20 </help>
21 <expand macro="citations" />
395 </tool> 22 </tool>