|
0
|
1 <tool id="msconvert2" name="msconvert2" version="0.1.0">
|
|
|
2 <!-- BEGIN_VERSION_DEFAULT -->
|
|
|
3 <description>Convert and filter a mass spec peak list</description>
|
|
|
4 <!-- END_VERSION_DEFAULT -->
|
|
|
5
|
|
|
6 <command interpreter="python">
|
|
|
7 msconvert_wrapper.py
|
|
|
8 --input=${input}
|
|
|
9 #if hasattr($input, 'display_name')
|
|
|
10 --input_name='${input.display_name}'
|
|
|
11 #end if
|
|
|
12 --output=${output}
|
|
|
13 ## BEGIN_VERSION_DEFAULT
|
|
|
14 --fromextension=${input.ext}
|
|
|
15 ## END_VERSION_DEFAULT
|
|
|
16
|
|
|
17
|
|
|
18 --toextension=${output_type}
|
|
|
19
|
|
|
20 #if $settings.settingsType == "full"
|
|
|
21 --binaryencoding=${settings.binary_encoding}
|
|
|
22 --mzencoding=${settings.mz_encoding}
|
|
|
23 --intensityencoding=${settings.intensity_encoding}
|
|
|
24 --zlib=${settings.zlib}
|
|
|
25 #end if
|
|
|
26
|
|
|
27 #if $filtering.filtering_use
|
|
|
28
|
|
|
29 #if $filtering.precursor_recalculation.value
|
|
|
30 --filter "precursorRecalculation"
|
|
|
31 #end if
|
|
|
32
|
|
|
33 #if $filtering.peak_picking.pick_peaks
|
|
|
34 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
|
|
|
35 #end if
|
|
|
36
|
|
|
37 #if str($filtering.activation) != "false"
|
|
|
38 --filter "activation $filtering.activation"
|
|
|
39 #end if
|
|
|
40
|
|
|
41 #if len($filtering.indices) > 0
|
|
|
42 --filter "index
|
|
|
43 #for $index in $filtering.indices
|
|
|
44 [${index.from},${index.to}]
|
|
|
45 #end for
|
|
|
46 "
|
|
|
47 #end if
|
|
|
48
|
|
|
49 #if len($filtering.scan_numbers) > 0
|
|
|
50 --filter "scanNumber
|
|
|
51 #for $scan_number in $filtering.scan_numbers
|
|
|
52 [${scan_number.from},${scan_number.to}]
|
|
|
53 #end for
|
|
|
54 "
|
|
|
55 #end if
|
|
|
56
|
|
|
57 #for threshold_entry in $filtering.threshold_repeat
|
|
|
58 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
|
|
|
59 #end for
|
|
|
60
|
|
|
61
|
|
|
62 #if $filtering.strip_it.value
|
|
|
63 --filter "stripIT"
|
|
|
64 #end if
|
|
|
65
|
|
|
66 #if $filtering.filter_mz_windows.do_filter
|
|
|
67 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
|
|
|
68 #end if
|
|
|
69
|
|
|
70
|
|
|
71 #if $filtering.filter_ms_levels.do_filter
|
|
|
72 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
|
|
|
73 #end if
|
|
|
74
|
|
|
75 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
|
|
|
76 --filter "ETDFilter"
|
|
|
77 #end if
|
|
|
78
|
|
|
79 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
|
|
|
80 --filter "ETDFilter removePrecursor:$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"
|
|
|
81 #end if
|
|
|
82
|
|
|
83
|
|
|
84 #end if
|
|
|
85
|
|
|
86 </command>
|
|
|
87
|
|
|
88 <inputs>
|
|
|
89
|
|
|
90 <!-- BEGIN_VERSION_DEFAULT -->
|
|
|
91 <conditional name="type">
|
|
|
92 <param name="input_type" type="select" label="Input Type">
|
|
|
93 <option value="mzml">mzML</option>
|
|
|
94 <option value="mzxml">mzXML</option>
|
|
|
95 <option value="mgf">mgf</option>
|
|
|
96 <option value="ms2">ms2</option>
|
|
|
97 </param>
|
|
|
98 <when value="mzml">
|
|
|
99 <param format="mzml" name="input" type="data" label="Input mzML"/>
|
|
|
100 </when>
|
|
|
101 <when value="mzxml">
|
|
|
102 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
|
|
|
103 </when>
|
|
|
104 <when value="mgf">
|
|
|
105 <param format="mgf" name="input" type="data" label="Input mgf"/>
|
|
|
106 </when>
|
|
|
107 <when value="ms2">
|
|
|
108 <param format="ms2" name="input" type="data" label="Input ms2"/>
|
|
|
109 </when>
|
|
|
110 </conditional>
|
|
|
111 <!-- END_VERSION_DEFAULT -->
|
|
|
112 <param name="output_type" type="select" label="Output Type">
|
|
|
113 <option value="mzML">mzML (indexed)</option>
|
|
|
114 <option value="unindexed_mzML">mzML (unindexed)</option>
|
|
|
115 <option value="mzXML">mzXML (indexed)</option>
|
|
|
116 <option value="unindexed_mzXML">mzXML (unindexed)</option>
|
|
|
117 <option value="mgf">mgf</option>
|
|
|
118 <option value="ms2">ms2</option>
|
|
|
119 </param>
|
|
|
120 <conditional name="filtering">
|
|
|
121 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
|
|
|
122 <when value="false" />
|
|
|
123 <when value="true">
|
|
|
124 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
|
|
|
125
|
|
|
126
|
|
|
127 <conditional name="peak_picking">
|
|
|
128 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
|
|
|
129 <when value="false" />
|
|
|
130 <when value="true">
|
|
|
131 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
|
|
|
132 <option value="1">MS1 Only (1)</option>
|
|
|
133 <option value="2">MS2 Only (2)</option>
|
|
|
134 <option value="2-">MS2 and on (2-)</option>
|
|
|
135 <option value="1-">All Levels (1-)</option>
|
|
|
136 </param>
|
|
|
137 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
|
|
|
138 </when>
|
|
|
139 </conditional>
|
|
|
140
|
|
|
141 <repeat name="threshold_repeat" title="Filter by Threshold">
|
|
|
142 <conditional name="threshold">
|
|
|
143 <param type="select" label="Specify threshold on" name="threshold_type" help="">
|
|
|
144 <option value="count">Peak count</option>
|
|
|
145 <option value="count-after-ties">Peak count (after ties)</option>
|
|
|
146 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
|
|
|
147 <option value="bpi-relative">Percent of base peak intensity</option>
|
|
|
148 <option value="tic-relative">Percent of total ion current</option>
|
|
|
149 <option value="tic-fraction">Aggregate percent of total ion current</option>
|
|
|
150 </param>
|
|
|
151 <when value="count">
|
|
|
152 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
|
|
|
153 </when>
|
|
|
154 <when value="count-after-ties">
|
|
|
155 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
|
|
|
156 </when>
|
|
|
157 <when value="absolute">
|
|
|
158 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
|
|
|
159 </when>
|
|
|
160 <when value="bpi-relative">
|
|
|
161 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
|
|
|
162 />
|
|
|
163 </when>
|
|
|
164 <when value="tic-relative">
|
|
|
165 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
|
|
|
166 />
|
|
|
167 </when>
|
|
|
168 <when value="tic-fraction">
|
|
|
169 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
|
|
|
170 </when>
|
|
|
171 </conditional>
|
|
|
172 <param type="select" label="Keep" name="orientation">
|
|
|
173 <option value="most-intense">Most intense peaks</option>
|
|
|
174 <option value="least-intense">Least intense peaks</option>
|
|
|
175 </param>
|
|
|
176 </repeat>
|
|
|
177
|
|
|
178
|
|
|
179 <param name="activation" type="select" label="Filter by Activation">
|
|
|
180 <option value="false" selected="true">no</option>
|
|
|
181 <option value="ETD">ETD</option>
|
|
|
182 <option value="CID">CID</option>
|
|
|
183 <option value="SA">SA</option>
|
|
|
184 <option value="HCD">HCD</option>
|
|
|
185 </param>
|
|
|
186
|
|
|
187 <repeat name="indices" title="Filter Scan Indices">
|
|
|
188 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
|
|
|
189 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
|
|
|
190 </repeat>
|
|
|
191
|
|
|
192 <repeat name="scan_numbers" title="Filter Scan Numbers">
|
|
|
193 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
|
|
|
194 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
|
|
|
195 </repeat>
|
|
|
196
|
|
|
197 <conditional name="filter_mz_windows">
|
|
|
198 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
|
|
|
199 <when value="false" />
|
|
|
200 <when value="true">
|
|
|
201 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
|
|
|
202 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
|
|
|
203 </when>
|
|
|
204 </conditional>
|
|
|
205
|
|
|
206 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
|
|
|
207
|
|
|
208 <conditional name="filter_ms_levels">
|
|
|
209 <param name="do_filter" type="boolean" label="Filter MS Levels" />
|
|
|
210 <when value="false" />
|
|
|
211 <when value="true">
|
|
|
212 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
|
|
|
213 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
|
|
|
214 </when>
|
|
|
215 </conditional>
|
|
|
216
|
|
|
217 <conditional name="etd_filtering">
|
|
|
218 <param name="do_etd_filtering" type="select" label="ETD Filtering">
|
|
|
219 <option value="none" selected="true">none</option>
|
|
|
220 <option value="default">yes (with default options)</option>
|
|
|
221 <option value="advanced">yes (show advanced options) </option>
|
|
|
222 </param>
|
|
|
223 <when value="none" />
|
|
|
224 <when value="default" />
|
|
|
225 <when value="advanced">
|
|
|
226 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
|
|
|
227 </param>
|
|
|
228 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
|
|
|
229 <option value="MZ" selected="true">mz</option>
|
|
|
230 <option value="PPM">ppm</option>
|
|
|
231 </param>
|
|
|
232 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
|
|
|
233 <option value="true" selected="true">yes</option>
|
|
|
234 <option value="false">no</option>
|
|
|
235 </param>
|
|
|
236 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
|
|
|
237 <option value="true" selected="true">yes</option>
|
|
|
238 <option value="false">no</option>
|
|
|
239 </param>
|
|
|
240 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
|
|
|
241 <option value="true" selected="true">yes</option>
|
|
|
242 <option value="false">no</option>
|
|
|
243 </param>
|
|
|
244 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
|
|
|
245 <option value="true" selected="true">yes</option>
|
|
|
246 <option value="false">no</option>
|
|
|
247 </param>
|
|
|
248 </when>
|
|
|
249 </conditional>
|
|
|
250
|
|
|
251
|
|
|
252 </when>
|
|
|
253 </conditional>
|
|
|
254
|
|
|
255 <conditional name="settings">
|
|
|
256 <param name="settingsType" type="select" label="Advanced Settings" help="">
|
|
|
257 <option value="default">Use Defaults</option>
|
|
|
258 <option value="full">Full Parameter List</option>
|
|
|
259 </param>
|
|
|
260 <when value="default" />
|
|
|
261 <when value="full">
|
|
|
262 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
|
|
|
263 <option value="64" selected="true">64</option>
|
|
|
264 <option value="32">32</option>
|
|
|
265 </param>
|
|
|
266 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
|
|
|
267 <option value="64" selected="true">64</option>
|
|
|
268 <option value="32">32</option>
|
|
|
269 </param>
|
|
|
270 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
|
|
|
271 <option value="64">64</option>
|
|
|
272 <option value="32" selected="true">32</option>
|
|
|
273 </param>
|
|
|
274 <param type="boolean" name="zlib" label="Use zlib">
|
|
|
275 </param>
|
|
|
276 </when>
|
|
|
277 </conditional>
|
|
|
278
|
|
|
279
|
|
|
280 </inputs>
|
|
|
281 <outputs>
|
|
|
282 <data format="mzml" name="output">
|
|
|
283 <change_format>
|
|
|
284 <when input="output_type" value="mzXML" format="mzxml" />
|
|
|
285 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
|
|
|
286 <when input="output_type" value="ms2" format="ms2" />
|
|
|
287 <when input="output_type" value="mgf" format="mgf" />
|
|
|
288 </change_format>
|
|
|
289 </data>
|
|
|
290 </outputs>
|
|
|
291
|
|
|
292 <requirements>
|
|
|
293 <requirement type="package">proteowizard</requirement>
|
|
|
294 </requirements>
|
|
|
295
|
|
|
296 <help>
|
|
|
297 **What it does**
|
|
|
298
|
|
|
299 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
|
|
|
300
|
|
|
301 You can view the original documentation here_.
|
|
|
302
|
|
|
303 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
|
|
|
304
|
|
|
305 ------
|
|
|
306
|
|
|
307 **Citation**
|
|
|
308
|
|
|
309 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.`
|
|
|
310
|
|
|
311 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
|
|
|
312
|
|
|
313 </help>
|
|
|
314 </tool>
|
