Mercurial > repos > galaxyp > msconvert
comparison msconvert2_raw.xml @ 0:10f4a0356342
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author | galaxyp |
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date | Wed, 19 Dec 2012 00:10:08 -0500 |
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children | 861e3f0c2bb6 |
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-1:000000000000 | 0:10f4a0356342 |
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1 <tool id="msconvert2_raw" name="msconvert2_raw" version="0.1.0"> | |
2 <!-- BEGIN_VERSION_RAW --> | |
3 <description>Convert and filter a Thermo Finnigan RAW file</description> | |
4 <!-- END_VERSION_RAW --> | |
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 | |
14 ## BEGIN_VERSION_RAW | |
15 --fromextension=RAW | |
16 ## END_VERSION_RAW | |
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 <!-- BEGIN_VERSION_RAW --> | |
90 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> | |
91 <!-- END_VERSION_RAW --> | |
92 | |
93 <param name="output_type" type="select" label="Output Type"> | |
94 <option value="mzML">mzML (indexed)</option> | |
95 <option value="unindexed_mzML">mzML (unindexed)</option> | |
96 <option value="mzXML">mzXML (indexed)</option> | |
97 <option value="unindexed_mzXML">mzXML (unindexed)</option> | |
98 <option value="mgf">mgf</option> | |
99 <option value="ms2">ms2</option> | |
100 </param> | |
101 <conditional name="filtering"> | |
102 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> | |
103 <when value="false" /> | |
104 <when value="true"> | |
105 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> | |
106 | |
107 | |
108 <conditional name="peak_picking"> | |
109 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> | |
110 <when value="false" /> | |
111 <when value="true"> | |
112 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> | |
113 <option value="1">MS1 Only (1)</option> | |
114 <option value="2">MS2 Only (2)</option> | |
115 <option value="2-">MS2 and on (2-)</option> | |
116 <option value="1-">All Levels (1-)</option> | |
117 </param> | |
118 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> | |
119 </when> | |
120 </conditional> | |
121 | |
122 <repeat name="threshold_repeat" title="Filter by Threshold"> | |
123 <conditional name="threshold"> | |
124 <param type="select" label="Specify threshold on" name="threshold_type" help=""> | |
125 <option value="count">Peak count</option> | |
126 <option value="count-after-ties">Peak count (after ties)</option> | |
127 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> | |
128 <option value="bpi-relative">Percent of base peak intensity</option> | |
129 <option value="tic-relative">Percent of total ion current</option> | |
130 <option value="tic-fraction">Aggregate percent of total ion current</option> | |
131 </param> | |
132 <when value="count"> | |
133 <param type="integer" name="value" label="Number of peaks to keep" value="100" /> | |
134 </when> | |
135 <when value="count-after-ties"> | |
136 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> | |
137 </when> | |
138 <when value="absolute"> | |
139 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> | |
140 </when> | |
141 <when value="bpi-relative"> | |
142 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" | |
143 /> | |
144 </when> | |
145 <when value="tic-relative"> | |
146 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" | |
147 /> | |
148 </when> | |
149 <when value="tic-fraction"> | |
150 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> | |
151 </when> | |
152 </conditional> | |
153 <param type="select" label="Keep" name="orientation"> | |
154 <option value="most-intense">Most intense peaks</option> | |
155 <option value="least-intense">Least intense peaks</option> | |
156 </param> | |
157 </repeat> | |
158 | |
159 | |
160 <param name="activation" type="select" label="Filter by Activation"> | |
161 <option value="false" selected="true">no</option> | |
162 <option value="ETD">ETD</option> | |
163 <option value="CID">CID</option> | |
164 <option value="SA">SA</option> | |
165 <option value="HCD">HCD</option> | |
166 </param> | |
167 | |
168 <repeat name="indices" title="Filter Scan Indices"> | |
169 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> | |
170 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> | |
171 </repeat> | |
172 | |
173 <repeat name="scan_numbers" title="Filter Scan Numbers"> | |
174 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> | |
175 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> | |
176 </repeat> | |
177 | |
178 <conditional name="filter_mz_windows"> | |
179 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> | |
180 <when value="false" /> | |
181 <when value="true"> | |
182 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> | |
183 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> | |
184 </when> | |
185 </conditional> | |
186 | |
187 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> | |
188 | |
189 <conditional name="filter_ms_levels"> | |
190 <param name="do_filter" type="boolean" label="Filter MS Levels" /> | |
191 <when value="false" /> | |
192 <when value="true"> | |
193 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> | |
194 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> | |
195 </when> | |
196 </conditional> | |
197 | |
198 <conditional name="etd_filtering"> | |
199 <param name="do_etd_filtering" type="select" label="ETD Filtering"> | |
200 <option value="none" selected="true">none</option> | |
201 <option value="default">yes (with default options)</option> | |
202 <option value="advanced">yes (show advanced options) </option> | |
203 </param> | |
204 <when value="none" /> | |
205 <when value="default" /> | |
206 <when value="advanced"> | |
207 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> | |
208 </param> | |
209 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> | |
210 <option value="MZ" selected="true">mz</option> | |
211 <option value="PPM">ppm</option> | |
212 </param> | |
213 <param name="remove_precursor" type="select" label="ETD Remove Precursor"> | |
214 <option value="true" selected="true">yes</option> | |
215 <option value="false">no</option> | |
216 </param> | |
217 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> | |
218 <option value="true" selected="true">yes</option> | |
219 <option value="false">no</option> | |
220 </param> | |
221 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> | |
222 <option value="true" selected="true">yes</option> | |
223 <option value="false">no</option> | |
224 </param> | |
225 <param name="blanket_removal" type="select" label="ETD Blanket Removal"> | |
226 <option value="true" selected="true">yes</option> | |
227 <option value="false">no</option> | |
228 </param> | |
229 </when> | |
230 </conditional> | |
231 | |
232 | |
233 </when> | |
234 </conditional> | |
235 | |
236 <conditional name="settings"> | |
237 <param name="settingsType" type="select" label="Advanced Settings" help=""> | |
238 <option value="default">Use Defaults</option> | |
239 <option value="full">Full Parameter List</option> | |
240 </param> | |
241 <when value="default" /> | |
242 <when value="full"> | |
243 <param type="select" name="binary_encoding" label="Binary Encoding Precision"> | |
244 <option value="64" selected="true">64</option> | |
245 <option value="32">32</option> | |
246 </param> | |
247 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> | |
248 <option value="64" selected="true">64</option> | |
249 <option value="32">32</option> | |
250 </param> | |
251 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> | |
252 <option value="64">64</option> | |
253 <option value="32" selected="true">32</option> | |
254 </param> | |
255 <param type="boolean" name="zlib" label="Use zlib"> | |
256 </param> | |
257 </when> | |
258 </conditional> | |
259 | |
260 | |
261 </inputs> | |
262 <outputs> | |
263 <data format="mzml" name="output"> | |
264 <change_format> | |
265 <when input="output_type" value="mzXML" format="mzxml" /> | |
266 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> | |
267 <when input="output_type" value="ms2" format="ms2" /> | |
268 <when input="output_type" value="mgf" format="mgf" /> | |
269 </change_format> | |
270 </data> | |
271 </outputs> | |
272 | |
273 <requirements> | |
274 <requirement type="package">proteowizard</requirement> | |
275 </requirements> | |
276 | |
277 <help> | |
278 **What it does** | |
279 | |
280 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. | |
281 | |
282 You can view the original documentation here_. | |
283 | |
284 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | |
285 | |
286 ------ | |
287 | |
288 **Citation** | |
289 | |
290 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.` | |
291 | |
292 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert | |
293 | |
294 </help> | |
295 </tool> |