Mercurial > repos > galaxyp > msconvert
comparison msconvert.xml @ 6:6b6bba73eadb draft
planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
author | galaxyp |
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date | Tue, 14 Mar 2017 16:52:39 -0400 |
parents | 637e309295cf |
children | e638f7fad66a |
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5:637e309295cf | 6:6b6bba73eadb |
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1 <tool id="msconvert" name="msconvert" version="0.3.0"> | 1 <tool id="msconvert" name="msconvert" version="0.3.0"> |
2 <description>Convert and/or filter mass spectrometry files</description> | 2 <!-- BEGIN_VERSION_DEFAULT --> |
3 | 3 <description>Convert and filter a mass spec peak list</description> |
4 <macros> | 4 <!-- END_VERSION_DEFAULT --> |
5 <import>msconvert_macros.xml</import> | 5 <!-- |
6 </macros> | |
7 | |
8 <requirements> | 6 <requirements> |
9 <requirement type="package" version="3.0.9992">proteowizard</requirement> | 7 <requirement type="package" version="3_0_4388">proteowizard</requirement> |
10 </requirements> | 8 </requirements> |
11 | 9 --> |
12 <expand macro="msconvertCommand" /> | 10 <command interpreter="python"> |
13 | 11 #import re |
14 <inputs> | 12 #set $ext = $input.ext |
15 <param format="mzml,mzxml,mz5,mgf,ms2" name="input" type="data" label="Input unrefined MS data" /> | 13 msconvert_wrapper.py |
16 | 14 #if $type.input_type == 'wiff': |
17 <expand macro="msconvertInputParameters" /> | 15 #set basename = 'absciex' |
16 #if hasattr($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 | |
18 </inputs> | 365 </inputs> |
19 | 366 <outputs> |
20 <expand macro="msconvertOutput" /> | 367 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > |
21 | 368 <change_format> |
22 <tests> | 369 <when input="output_type" value="mzXML" format="mzxml" /> |
23 <test> | 370 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> |
24 <param name="input" value="small.mzML" /> | 371 <when input="output_type" value="ms2" format="ms2" /> |
25 <param name="output_type" value="mzML" /> | 372 <when input="output_type" value="mgf" format="mgf" /> |
26 <param name="pick_peaks" value="true" /> | 373 </change_format> |
27 <param name="pick_peaks_algorithm" value="cwt" /> | 374 </data> |
28 <param name="pick_peaks_ms_levels" value="1-" /> | 375 </outputs> |
29 <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> | |
30 </test> | |
31 | |
32 <!-- this data file only has profile MS1, so the result is the same --> | |
33 <test> | |
34 <param name="input" value="small.mzML" /> | |
35 <param name="output_type" value="mzML" /> | |
36 <param name="pick_peaks" value="true" /> | |
37 <param name="pick_peaks_algorithm" value="cwt" /> | |
38 <param name="pick_peaks_ms_levels" value="1" /> | |
39 <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> | |
40 </test> | |
41 <test> | |
42 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
43 <param name="output_type" value="mz5" /> | |
44 <param name="mz_encoding" value="64" /> | |
45 <param name="intensity_encoding" value="64" /> | |
46 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" /> | |
47 </test> | |
48 <test> | |
49 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
50 <param name="output_type" value="mzXML" /> | |
51 <param name="mz_encoding" value="32" /> | |
52 <param name="intensity_encoding" value="32" /> | |
53 <output name="output" file="small-zlib-32.mzXML" /> | |
54 </test> | |
55 <!-- TODO: how to test gzipped output? | |
56 <test> | |
57 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
58 <param name="output_type" value="mzXML" /> | |
59 <param name="mz_encoding" value="32" /> | |
60 <param name="intensity_encoding" value="32" /> | |
61 <param name="binary_compression" value="false" /> | |
62 <param name="gzip_compression" value="true" /> | |
63 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" /> | |
64 </test> | |
65 <test> | |
66 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
67 <param name="output_type" value="mzML" /> | |
68 <param name="mz_encoding" value="32" /> | |
69 <param name="intensity_encoding" value="32" /> | |
70 <param name="binary_compression" value="false" /> | |
71 <param name="gzip_compression" value="true" /> | |
72 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> | |
73 </test>--> | |
74 | |
75 <test> | |
76 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
77 <param name="output_type" value="mzML" /> | |
78 <param name="binary_compression" value="numpressLinearPic" /> | |
79 <output name="output" file="small-numpressLP.mzML" /> | |
80 </test> | |
81 | |
82 <test> | |
83 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
84 <param name="output_type" value="mzML" /> | |
85 <param name="binary_compression" value="numpressLinearSlof" /> | |
86 <output name="output" file="small-numpressLS.mzML" /> | |
87 </test> | |
88 | |
89 <test> | |
90 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
91 <param name="output_type" value="mzML" /> | |
92 <param name="binary_compression" value="numpressLinear" /> | |
93 <output name="output" file="small-numpressL.mzML" /> | |
94 </test> | |
95 | |
96 <test> | |
97 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
98 <param name="output_type" value="mzML" /> | |
99 <param name="binary_compression" value="numpressPic" /> | |
100 <output name="output" file="small-numpressP.mzML" /> | |
101 </test> | |
102 | |
103 <test> | |
104 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
105 <param name="output_type" value="mzML" /> | |
106 <param name="binary_compression" value="numpressSlof" /> | |
107 <output name="output" file="small-numpressS.mzML" /> | |
108 </test> | |
109 | |
110 <test> | |
111 <param name="input" value="Rpal_01.mz5" /> | |
112 <param name="output_type" value="mzML" /> | |
113 <param name="binary_compression" value="numpressLinearPic" /> | |
114 <param name="use_mzrefinement" value="true" /> | |
115 <param name="input_ident" value="Rpal_01.pepXML.gz" /> | |
116 <param name="thresholdScore" value="mvh" /> | |
117 <param name="thresholdValue" value="40-" /> | |
118 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> | |
119 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> | |
120 </test> | |
121 | |
122 <test> | |
123 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
124 <param name="output_type" value="mzML" /> | |
125 <param name="binary_compression" value="numpressLinearPic" /> | |
126 <param name="charge_state_calculation_method" value="predictor" /> | |
127 <param name="predictor_overrideExistingCharge" value="true" /> | |
128 <param name="minMultipleCharge" value="2" /> | |
129 <param name="maxMultipleCharge" value="5" /> | |
130 <param name="singleChargeFractionTIC" value="0.95" /> | |
131 <param name="maxKnownCharge" value="8" /> | |
132 <output name="output" file="small-chargeStatePredictor.mzML" /> | |
133 </test> | |
134 <test> | |
135 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
136 <param name="output_type" value="mzML" /> | |
137 <param name="binary_compression" value="numpressLinearPic" /> | |
138 <param name="charge_state_calculation_method" value="turbocharger" /> | |
139 <param name="minCharge" value="1" /> | |
140 <param name="maxCharge" value="5" /> | |
141 <param name="precursorsBefore" value="1" /> | |
142 <param name="precursorsAfter" value="1" /> | |
143 <param name="halfIsoWidth" value="1.5" /> | |
144 <param name="defaultMinCharge" value="1" /> | |
145 <param name="defaultMaxCharge" value="5" /> | |
146 <output name="output" file="small-turbocharger.mzML" /> | |
147 </test> | |
148 <test> | |
149 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> | |
150 <param name="output_type" value="mzML" /> | |
151 <param name="do_etd_filtering" value="true" /> | |
152 <param name="remove_precursor" value="true" /> | |
153 <param name="remove_charge_reduced" value="true" /> | |
154 <param name="remove_neutral_loss" value="false" /> | |
155 <param name="blanket_removal" value="false" /> | |
156 <param name="matching_tolerance" value="50" /> | |
157 <param name="matching_tolerance_units" value="ppm" /> | |
158 <param name="binary_compression" value="numpressLinearPic" /> | |
159 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" /> | |
160 </test> | |
161 <test> | |
162 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
163 <param name="output_type" value="mzML" /> | |
164 <param name="thresholds_0|threshold_type" value="count" /> | |
165 <param name="thresholds_0|value" value="100" /> | |
166 <param name="thresholds_0|orientation" value="most-intense" /> | |
167 <param name="thresholds_1|threshold_type" value="absolute" /> | |
168 <param name="thresholds_1|value" value="1" /> | |
169 <param name="thresholds_1|orientation" value="most-intense" /> | |
170 <param name="binary_compression" value="numpressLinearPic" /> | |
171 <output name="output" file="small-threshold.mzML" /> | |
172 </test> | |
173 <test> | |
174 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
175 <param name="output_type" value="mzML" /> | |
176 <param name="do_mzwindow_filter" value="true" /> | |
177 <param name="mz_window_from" value="420" /> | |
178 <param name="mz_window_to" value="840" /> | |
179 <param name="binary_compression" value="numpressLinearPic" /> | |
180 <output name="output" file="small-mzWindow.mzML" /> | |
181 </test> | |
182 <test> | |
183 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
184 <param name="output_type" value="mzML" /> | |
185 <param name="denoise" value="true" /> | |
186 <param name="num_peaks" value="10" /> | |
187 <param name="window_width" value="40" /> | |
188 <param name="relax" value="false" /> | |
189 <param name="binary_compression" value="numpressLinearPic" /> | |
190 <output name="output" file="small-denoise.mzML" /> | |
191 </test> | |
192 <test> | |
193 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
194 <param name="output_type" value="mzML" /> | |
195 <param name="ms2deisotope" value="true" /> | |
196 <param name="binary_compression" value="numpressLinearPic" /> | |
197 <output name="output" file="small-deisotope.mzML" /> | |
198 </test> | |
199 <test> | |
200 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
201 <param name="output_type" value="mzML" /> | |
202 <param name="activation" value="CID" /> | |
203 <param name="binary_compression" value="numpressLinearPic" /> | |
204 <output name="output" file="small-activation.mzML" /> | |
205 </test> | |
206 <test> | |
207 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
208 <param name="output_type" value="mzML" /> | |
209 <param name="indices_0|from" value="2" /> | |
210 <param name="indices_0|to" value="4" /> | |
211 <param name="indices_1|from" value="10" /> | |
212 <param name="indices_1|to" value="10" /> | |
213 <param name="indices_2|from" value="13" /> | |
214 <param name="indices_2|to" value="15" /> | |
215 <param name="binary_compression" value="numpressLinearPic" /> | |
216 <output name="output" file="small-index-filter.mzML" /> | |
217 </test> | |
218 <test> | |
219 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
220 <param name="output_type" value="mzML" /> | |
221 <param name="strip_it" value="true" /> | |
222 <param name="binary_compression" value="numpressLinearPic" /> | |
223 <output name="output" file="small-strip-it.mzML" /> | |
224 </test> | |
225 <test> | |
226 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
227 <param name="output_type" value="mzML" /> | |
228 <param name="do_ms_level_filter" value="true" /> | |
229 <param name="ms_level_from" value="2" /> | |
230 <param name="ms_level_to" value="2" /> | |
231 <param name="binary_compression" value="numpressLinearPic" /> | |
232 <output name="output" file="small-ms-level-filter.mzML" /> | |
233 </test> | |
234 <test> | |
235 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
236 <param name="output_type" value="mzML" /> | |
237 <param name="polarity" value="positive" /> | |
238 <param name="binary_compression" value="numpressLinearPic" /> | |
239 <output name="output" file="small-polarity-filter.mzML" /> | |
240 </test> | |
241 <test> | |
242 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
243 <param name="output_type" value="mzML" /> | |
244 <param name="analyzer" value="IT" /> | |
245 <param name="binary_compression" value="numpressLinearPic" /> | |
246 <output name="output" file="small-analyzer-filter.mzML" /> | |
247 </test> | |
248 <test> | |
249 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
250 <param name="output_type" value="mzML" /> | |
251 <param name="scan_numbers_0|from" value="3" /> | |
252 <param name="scan_numbers_0|to" value="5" /> | |
253 <param name="scan_numbers_1|from" value="11" /> | |
254 <param name="scan_numbers_1|to" value="11" /> | |
255 <param name="scan_numbers_2|from" value="14" /> | |
256 <param name="scan_numbers_2|to" value="16" /> | |
257 <param name="binary_compression" value="numpressLinearPic" /> | |
258 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above --> | |
259 </test> | |
260 <!--<test> | |
261 <param name="input" value="small.mzML" /> | |
262 <param name="output_type" value="mzML" /> | |
263 <param name="binary_compression" value="numpressLinearPic" /> | |
264 <output name="output" file="small-deisotope-poisson.mzML" /> | |
265 </test>--> | |
266 </tests> | |
267 <help> | 376 <help> |
268 **What it does** | 377 **What it does** |
269 | 378 |
270 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. | 379 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. |
271 | 380 |
272 You can view the original documentation here_. | 381 You can view the original documentation here_. |
273 | 382 |
274 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | 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 | |
275 </help> | 394 </help> |
276 <citations> | |
277 <citation type="doi">10.1093/bioinformatics/btn323</citation> | |
278 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, | |
279 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> | |
280 </citations> | |
281 </tool> | 395 </tool> |