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comparison msconvert2_raw.xml @ 7:37e5502441cc draft

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author galaxyp
date Mon, 17 Feb 2014 17:00:29 -0500
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6:ffe1dca94595 7:37e5502441cc
1 <tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.1">
2 <!-- BEGIN_VERSION_RAW -->
3 <description>Convert and filter a Thermo Finnigan RAW file</description>
4 <!-- END_VERSION_RAW -->
5 <requirements>
6 <requirement type="package">proteowizard</requirement>
7 <!-- BEGIN_VERSION_RAW -->
8 <requirement type="platform">windows</requirement>
9 <!-- END_VERSION_RAW -->
10 </requirements>
11 <command interpreter="python">
12 #set $ext = $input.ext
13 #if $ext.startswith("m:")
14 #set $ext = $ext[len("m:"):]
15 #end if
16 msconvert_wrapper.py
17 --input=${input}
18 #if hasattr($input, 'display_name')
19 --input_name='${input.display_name}'
20 #end if
21 --output=${output}
22
23 ## BEGIN_VERSION_RAW
24 --fromextension=RAW
25 ## END_VERSION_RAW
26
27 --toextension=${output_type}
28
29 #if $settings.settingsType == "full"
30 --binaryencoding=${settings.binary_encoding}
31 --mzencoding=${settings.mz_encoding}
32 --intensityencoding=${settings.intensity_encoding}
33 --zlib=${settings.zlib}
34 #end if
35
36 #if $filtering.filtering_use
37
38 #if $filtering.precursor_recalculation.value
39 --filter "precursorRecalculation"
40 #end if
41
42 #if $filtering.peak_picking.pick_peaks
43 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
44 #end if
45
46 #if str($filtering.activation) != "false"
47 --filter "activation $filtering.activation"
48 #end if
49
50 #if len($filtering.indices) > 0
51 --filter "index
52 #for $index in $filtering.indices
53 [${index.from},${index.to}]
54 #end for
55 "
56 #end if
57
58 #if len($filtering.scan_numbers) > 0
59 --filter "scanNumber
60 #for $scan_number in $filtering.scan_numbers
61 [${scan_number.from},${scan_number.to}]
62 #end for
63 "
64 #end if
65
66 #for threshold_entry in $filtering.threshold_repeat
67 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
68 #end for
69
70
71 #if $filtering.strip_it.value
72 --filter "stripIT"
73 #end if
74
75 #if $filtering.filter_mz_windows.do_filter
76 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
77 #end if
78
79
80 #if $filtering.filter_ms_levels.do_filter
81 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
82 #end if
83
84 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
85 --filter "ETDFilter"
86 #end if
87
88 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
89 --filter "ETDFilter removePrecursor:$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"
90 #end if
91
92
93 #end if
94
95 </command>
96
97 <inputs>
98 <!-- BEGIN_VERSION_RAW -->
99 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
100 <!-- END_VERSION_RAW -->
101
102 <param name="output_type" type="select" label="Output Type">
103 <option value="mzML">mzML (indexed)</option>
104 <option value="unindexed_mzML">mzML (unindexed)</option>
105 <option value="mzXML">mzXML (indexed)</option>
106 <option value="unindexed_mzXML">mzXML (unindexed)</option>
107 <option value="mgf">mgf</option>
108 <option value="ms2">ms2</option>
109 </param>
110 <conditional name="filtering">
111 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
112 <when value="false" />
113 <when value="true">
114 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
115
116
117 <conditional name="peak_picking">
118 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
119 <when value="false" />
120 <when value="true">
121 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
122 <option value="1">MS1 Only (1)</option>
123 <option value="2">MS2 Only (2)</option>
124 <option value="2-">MS2 and on (2-)</option>
125 <option value="1-">All Levels (1-)</option>
126 </param>
127 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
128 </when>
129 </conditional>
130
131 <repeat name="threshold_repeat" title="Filter by Threshold">
132 <conditional name="threshold">
133 <param type="select" label="Specify threshold on" name="threshold_type" help="">
134 <option value="count">Peak count</option>
135 <option value="count-after-ties">Peak count (after ties)</option>
136 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
137 <option value="bpi-relative">Percent of base peak intensity</option>
138 <option value="tic-relative">Percent of total ion current</option>
139 <option value="tic-fraction">Aggregate percent of total ion current</option>
140 </param>
141 <when value="count">
142 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
143 </when>
144 <when value="count-after-ties">
145 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
146 </when>
147 <when value="absolute">
148 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
149 </when>
150 <when value="bpi-relative">
151 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
152 />
153 </when>
154 <when value="tic-relative">
155 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
156 />
157 </when>
158 <when value="tic-fraction">
159 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
160 </when>
161 </conditional>
162 <param type="select" label="Keep" name="orientation">
163 <option value="most-intense">Most intense peaks</option>
164 <option value="least-intense">Least intense peaks</option>
165 </param>
166 </repeat>
167
168
169 <param name="activation" type="select" label="Filter by Activation">
170 <option value="false" selected="true">no</option>
171 <option value="ETD">ETD</option>
172 <option value="CID">CID</option>
173 <option value="SA">SA</option>
174 <option value="HCD">HCD</option>
175 </param>
176
177 <repeat name="indices" title="Filter Scan Indices">
178 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
179 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
180 </repeat>
181
182 <repeat name="scan_numbers" title="Filter Scan Numbers">
183 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
184 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
185 </repeat>
186
187 <conditional name="filter_mz_windows">
188 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
189 <when value="false" />
190 <when value="true">
191 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
192 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
193 </when>
194 </conditional>
195
196 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
197
198 <conditional name="filter_ms_levels">
199 <param name="do_filter" type="boolean" label="Filter MS Levels" />
200 <when value="false" />
201 <when value="true">
202 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
203 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
204 </when>
205 </conditional>
206
207 <conditional name="etd_filtering">
208 <param name="do_etd_filtering" type="select" label="ETD Filtering">
209 <option value="none" selected="true">none</option>
210 <option value="default">yes (with default options)</option>
211 <option value="advanced">yes (show advanced options) </option>
212 </param>
213 <when value="none" />
214 <when value="default" />
215 <when value="advanced">
216 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
217 </param>
218 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
219 <option value="MZ" selected="true">mz</option>
220 <option value="PPM">ppm</option>
221 </param>
222 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
223 <option value="true" selected="true">yes</option>
224 <option value="false">no</option>
225 </param>
226 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
227 <option value="true" selected="true">yes</option>
228 <option value="false">no</option>
229 </param>
230 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
231 <option value="true" selected="true">yes</option>
232 <option value="false">no</option>
233 </param>
234 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
235 <option value="true" selected="true">yes</option>
236 <option value="false">no</option>
237 </param>
238 </when>
239 </conditional>
240
241
242 </when>
243 </conditional>
244
245 <conditional name="settings">
246 <param name="settingsType" type="select" label="Advanced Settings" help="">
247 <option value="default">Use Defaults</option>
248 <option value="full">Full Parameter List</option>
249 </param>
250 <when value="default" />
251 <when value="full">
252 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
253 <option value="64" selected="true">64</option>
254 <option value="32">32</option>
255 </param>
256 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
257 <option value="64" selected="true">64</option>
258 <option value="32">32</option>
259 </param>
260 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
261 <option value="64">64</option>
262 <option value="32" selected="true">32</option>
263 </param>
264 <param type="boolean" name="zlib" label="Use zlib">
265 </param>
266 </when>
267 </conditional>
268
269
270 </inputs>
271 <outputs>
272 <data format="mzml" name="output">
273 <change_format>
274 <when input="output_type" value="mzXML" format="mzxml" />
275 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
276 <when input="output_type" value="ms2" format="ms2" />
277 <when input="output_type" value="mgf" format="mgf" />
278 </change_format>
279 </data>
280 </outputs>
281 <help>
282 **What it does**
283
284 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
285
286 You can view the original documentation here_.
287
288 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
289
290 ------
291
292 **Citation**
293
294 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.`
295
296 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
297
298 </help>
299 </tool>