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comparison msconvert2.xml @ 0:10f4a0356342

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author galaxyp
date Wed, 19 Dec 2012 00:10:08 -0500
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-1:000000000000 0:10f4a0356342
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>