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comparison IsobaricAnalyzer.xml @ 0:916f41a35640 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:22:29 -0500
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children 125774c3e8aa
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-1:000000000000 0:916f41a35640
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.1.0">
5 <description>Calculates isobaric quantitative values for peptides</description>
6 <macros>
7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IsobaricAnalyzer
14
15 #if $param_type:
16 -type $param_type
17 #end if
18 #if $param_in:
19 -in $param_in
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_id_pool:
25 -id_pool "$param_id_pool"
26 #end if
27 #if $param_extraction_select_activation:
28 -extraction:select_activation $param_extraction_select_activation
29 #end if
30 #if $param_extraction_reporter_mass_shift:
31 -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
32 #end if
33 #if $param_extraction_min_precursor_intensity:
34 -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
35 #end if
36 #if $param_extraction_keep_unannotated_precursor:
37 -extraction:keep_unannotated_precursor $param_extraction_keep_unannotated_precursor
38 #end if
39 #if $param_extraction_min_reporter_intensity:
40 -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
41 #end if
42 #if $param_extraction_discard_low_intensity_quantifications:
43 -extraction:discard_low_intensity_quantifications
44 #end if
45 #if $param_extraction_min_precursor_purity:
46 -extraction:min_precursor_purity $param_extraction_min_precursor_purity
47 #end if
48 #if $param_itraq4plex_channel_114_description:
49 -itraq4plex:channel_114_description "$param_itraq4plex_channel_114_description"
50 #end if
51 #if $param_itraq4plex_channel_115_description:
52 -itraq4plex:channel_115_description "$param_itraq4plex_channel_115_description"
53 #end if
54 #if $param_itraq4plex_channel_116_description:
55 -itraq4plex:channel_116_description "$param_itraq4plex_channel_116_description"
56 #end if
57 #if $param_itraq4plex_channel_117_description:
58 -itraq4plex:channel_117_description "$param_itraq4plex_channel_117_description"
59 #end if
60 #if $param_itraq4plex_reference_channel:
61 -itraq4plex:reference_channel $param_itraq4plex_reference_channel
62 #end if
63
64 #if $rep_param_itraq4plex_correction_matrix:
65 -itraq4plex:correction_matrix
66 #for token in $rep_param_itraq4plex_correction_matrix:
67 #if " " in str(token):
68 "$token.param_itraq4plex_correction_matrix"
69 #else
70 $token.param_itraq4plex_correction_matrix
71 #end if
72 #end for
73 #end if
74 #if $param_itraq8plex_channel_113_description:
75 -itraq8plex:channel_113_description "$param_itraq8plex_channel_113_description"
76 #end if
77 #if $param_itraq8plex_channel_114_description:
78 -itraq8plex:channel_114_description "$param_itraq8plex_channel_114_description"
79 #end if
80 #if $param_itraq8plex_channel_115_description:
81 -itraq8plex:channel_115_description "$param_itraq8plex_channel_115_description"
82 #end if
83 #if $param_itraq8plex_channel_116_description:
84 -itraq8plex:channel_116_description "$param_itraq8plex_channel_116_description"
85 #end if
86 #if $param_itraq8plex_channel_117_description:
87 -itraq8plex:channel_117_description "$param_itraq8plex_channel_117_description"
88 #end if
89 #if $param_itraq8plex_channel_118_description:
90 -itraq8plex:channel_118_description "$param_itraq8plex_channel_118_description"
91 #end if
92 #if $param_itraq8plex_channel_119_description:
93 -itraq8plex:channel_119_description "$param_itraq8plex_channel_119_description"
94 #end if
95 #if $param_itraq8plex_channel_121_description:
96 -itraq8plex:channel_121_description "$param_itraq8plex_channel_121_description"
97 #end if
98 #if $param_itraq8plex_reference_channel:
99 -itraq8plex:reference_channel $param_itraq8plex_reference_channel
100 #end if
101
102 #if $rep_param_itraq8plex_correction_matrix:
103 -itraq8plex:correction_matrix
104 #for token in $rep_param_itraq8plex_correction_matrix:
105 #if " " in str(token):
106 "$token.param_itraq8plex_correction_matrix"
107 #else
108 $token.param_itraq8plex_correction_matrix
109 #end if
110 #end for
111 #end if
112 #if $param_quantification_isotope_correction:
113 -quantification:isotope_correction $param_quantification_isotope_correction
114 #end if
115 #if $param_quantification_normalization:
116 -quantification:normalization
117 #end if
118 #if $param_tmt10plex_channel_126_description:
119 -tmt10plex:channel_126_description "$param_tmt10plex_channel_126_description"
120 #end if
121 #if $param_tmt10plex_channel_127N_description:
122 -tmt10plex:channel_127N_description "$param_tmt10plex_channel_127N_description"
123 #end if
124 #if $param_tmt10plex_channel_127C_description:
125 -tmt10plex:channel_127C_description "$param_tmt10plex_channel_127C_description"
126 #end if
127 #if $param_tmt10plex_channel_128N_description:
128 -tmt10plex:channel_128N_description "$param_tmt10plex_channel_128N_description"
129 #end if
130 #if $param_tmt10plex_channel_128C_description:
131 -tmt10plex:channel_128C_description "$param_tmt10plex_channel_128C_description"
132 #end if
133 #if $param_tmt10plex_channel_129N_description:
134 -tmt10plex:channel_129N_description "$param_tmt10plex_channel_129N_description"
135 #end if
136 #if $param_tmt10plex_channel_129C_description:
137 -tmt10plex:channel_129C_description "$param_tmt10plex_channel_129C_description"
138 #end if
139 #if $param_tmt10plex_channel_130N_description:
140 -tmt10plex:channel_130N_description "$param_tmt10plex_channel_130N_description"
141 #end if
142 #if $param_tmt10plex_channel_130C_description:
143 -tmt10plex:channel_130C_description "$param_tmt10plex_channel_130C_description"
144 #end if
145 #if $param_tmt10plex_channel_131_description:
146 -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description"
147 #end if
148 #if $param_tmt10plex_reference_channel:
149 -tmt10plex:reference_channel $param_tmt10plex_reference_channel
150 #end if
151
152 #if $rep_param_tmt10plex_correction_matrix:
153 -tmt10plex:correction_matrix
154 #for token in $rep_param_tmt10plex_correction_matrix:
155 #if " " in str(token):
156 "$token.param_tmt10plex_correction_matrix"
157 #else
158 $token.param_tmt10plex_correction_matrix
159 #end if
160 #end for
161 #end if
162 #if $param_tmt6plex_channel_126_description:
163 -tmt6plex:channel_126_description "$param_tmt6plex_channel_126_description"
164 #end if
165 #if $param_tmt6plex_channel_127_description:
166 -tmt6plex:channel_127_description "$param_tmt6plex_channel_127_description"
167 #end if
168 #if $param_tmt6plex_channel_128_description:
169 -tmt6plex:channel_128_description "$param_tmt6plex_channel_128_description"
170 #end if
171 #if $param_tmt6plex_channel_129_description:
172 -tmt6plex:channel_129_description "$param_tmt6plex_channel_129_description"
173 #end if
174 #if $param_tmt6plex_channel_130_description:
175 -tmt6plex:channel_130_description "$param_tmt6plex_channel_130_description"
176 #end if
177 #if $param_tmt6plex_channel_131_description:
178 -tmt6plex:channel_131_description "$param_tmt6plex_channel_131_description"
179 #end if
180 #if $param_tmt6plex_reference_channel:
181 -tmt6plex:reference_channel $param_tmt6plex_reference_channel
182 #end if
183
184 #if $rep_param_tmt6plex_correction_matrix:
185 -tmt6plex:correction_matrix
186 #for token in $rep_param_tmt6plex_correction_matrix:
187 #if " " in str(token):
188 "$token.param_tmt6plex_correction_matrix"
189 #else
190 $token.param_tmt6plex_correction_matrix
191 #end if
192 #end for
193 #end if
194 #if $adv_opts.adv_opts_selector=='advanced':
195 #if $adv_opts.param_force:
196 -force
197 #end if
198 #if $adv_opts.param_extraction_precursor_isotope_deviation:
199 -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
200 #end if
201 #if $adv_opts.param_extraction_purity_interpolation:
202 -extraction:purity_interpolation $adv_opts.param_extraction_purity_interpolation
203 #end if
204 #end if
205 </command>
206 <inputs>
207 <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
208 <option value="itraq4plex" selected="true">itraq4plex</option>
209 <option value="itraq8plex">itraq8plex</option>
210 <option value="tmt10plex">tmt10plex</option>
211 <option value="tmt6plex">tmt6plex</option>
212 </param>
213 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
214 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)">
215 <sanitizer>
216 <valid initial="string.printable">
217 <remove value="'"/>
218 <remove value="&quot;"/>
219 </valid>
220 </sanitizer>
221 </param>
222 <param name="param_extraction_select_activation" type="select" optional="False" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (" help="(-select_activation) e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering">
223 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
224 <option value="Post-source decay">Post-source decay</option>
225 <option value="Plasma desorption">Plasma desorption</option>
226 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
227 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
228 <option value="Electron capture dissociation">Electron capture dissociation</option>
229 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
230 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
231 <option value="High-energy collision-induced dissociation" selected="true">High-energy collision-induced dissociation</option>
232 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
233 <option value="Photodissociation">Photodissociation</option>
234 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
235 <option value=""></option>
236 </param>
237 <param name="param_extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/>
238 <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
239 <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) ">
240 <option value="true" selected="true">true</option>
241 <option value="false">false</option>
242 </param>
243 <param name="param_extraction_min_reporter_intensity" type="float" min="0.0" optional="True" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help="(-min_reporter_intensity) "/>
244 <param name="param_extraction_discard_low_intensity_quantifications" display="radio" type="boolean" truevalue="-extraction:discard_low_intensity_quantifications" falsevalue="" checked="false" optional="True" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help="(-discard_low_intensity_quantifications) "/>
245 <param name="param_extraction_min_precursor_purity" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help="(-min_precursor_purity) "/>
246 <param name="param_itraq4plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) ">
247 <sanitizer>
248 <valid initial="string.printable">
249 <remove value="'"/>
250 <remove value="&quot;"/>
251 </valid>
252 </sanitizer>
253 </param>
254 <param name="param_itraq4plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) ">
255 <sanitizer>
256 <valid initial="string.printable">
257 <remove value="'"/>
258 <remove value="&quot;"/>
259 </valid>
260 </sanitizer>
261 </param>
262 <param name="param_itraq4plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) ">
263 <sanitizer>
264 <valid initial="string.printable">
265 <remove value="'"/>
266 <remove value="&quot;"/>
267 </valid>
268 </sanitizer>
269 </param>
270 <param name="param_itraq4plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) ">
271 <sanitizer>
272 <valid initial="string.printable">
273 <remove value="'"/>
274 <remove value="&quot;"/>
275 </valid>
276 </sanitizer>
277 </param>
278 <param name="param_itraq4plex_reference_channel" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117)" help="(-reference_channel) "/>
279 <repeat name="rep_param_itraq4plex_correction_matrix" min="0" max="1" title="param_itraq4plex_correction_matrix">
280 <param name="param_itraq4plex_correction_matrix" type="text" size="30" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
281 <sanitizer>
282 <valid initial="string.printable">
283 <remove value="'"/>
284 <remove value="&quot;"/>
285 </valid>
286 </sanitizer>
287 </param>
288 </repeat>
289 <param name="param_itraq8plex_channel_113_description" type="text" size="30" label="Description for the content of the 113 channel" help="(-channel_113_description) ">
290 <sanitizer>
291 <valid initial="string.printable">
292 <remove value="'"/>
293 <remove value="&quot;"/>
294 </valid>
295 </sanitizer>
296 </param>
297 <param name="param_itraq8plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) ">
298 <sanitizer>
299 <valid initial="string.printable">
300 <remove value="'"/>
301 <remove value="&quot;"/>
302 </valid>
303 </sanitizer>
304 </param>
305 <param name="param_itraq8plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) ">
306 <sanitizer>
307 <valid initial="string.printable">
308 <remove value="'"/>
309 <remove value="&quot;"/>
310 </valid>
311 </sanitizer>
312 </param>
313 <param name="param_itraq8plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) ">
314 <sanitizer>
315 <valid initial="string.printable">
316 <remove value="'"/>
317 <remove value="&quot;"/>
318 </valid>
319 </sanitizer>
320 </param>
321 <param name="param_itraq8plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) ">
322 <sanitizer>
323 <valid initial="string.printable">
324 <remove value="'"/>
325 <remove value="&quot;"/>
326 </valid>
327 </sanitizer>
328 </param>
329 <param name="param_itraq8plex_channel_118_description" type="text" size="30" label="Description for the content of the 118 channel" help="(-channel_118_description) ">
330 <sanitizer>
331 <valid initial="string.printable">
332 <remove value="'"/>
333 <remove value="&quot;"/>
334 </valid>
335 </sanitizer>
336 </param>
337 <param name="param_itraq8plex_channel_119_description" type="text" size="30" label="Description for the content of the 119 channel" help="(-channel_119_description) ">
338 <sanitizer>
339 <valid initial="string.printable">
340 <remove value="'"/>
341 <remove value="&quot;"/>
342 </valid>
343 </sanitizer>
344 </param>
345 <param name="param_itraq8plex_channel_121_description" type="text" size="30" label="Description for the content of the 121 channel" help="(-channel_121_description) ">
346 <sanitizer>
347 <valid initial="string.printable">
348 <remove value="'"/>
349 <remove value="&quot;"/>
350 </valid>
351 </sanitizer>
352 </param>
353 <param name="param_itraq8plex_reference_channel" type="integer" min="113" max="121" optional="True" value="113" label="Number of the reference channel (113-121)" help="(-reference_channel) Please note that 120 is not valid"/>
354 <repeat name="rep_param_itraq8plex_correction_matrix" min="0" max="1" title="param_itraq8plex_correction_matrix">
355 <param name="param_itraq8plex_correction_matrix" type="text" size="30" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
356 <sanitizer>
357 <valid initial="string.printable">
358 <remove value="'"/>
359 <remove value="&quot;"/>
360 </valid>
361 </sanitizer>
362 </param>
363 </repeat>
364 <param name="param_quantification_isotope_correction" display="radio" type="select" optional="False" value="true" label="Enable isotope correction (highly recommended)" help="(-isotope_correction) Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results">
365 <option value="true" selected="true">true</option>
366 <option value="false">false</option>
367 </param>
368 <param name="param_quantification_normalization" display="radio" type="boolean" truevalue="-quantification:normalization" falsevalue="" checked="false" optional="True" label="Enable normalization of channel intensities with respect to the reference channel" help="(-normalization) The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/>
369 <param name="param_tmt10plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
370 <sanitizer>
371 <valid initial="string.printable">
372 <remove value="'"/>
373 <remove value="&quot;"/>
374 </valid>
375 </sanitizer>
376 </param>
377 <param name="param_tmt10plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) ">
378 <sanitizer>
379 <valid initial="string.printable">
380 <remove value="'"/>
381 <remove value="&quot;"/>
382 </valid>
383 </sanitizer>
384 </param>
385 <param name="param_tmt10plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) ">
386 <sanitizer>
387 <valid initial="string.printable">
388 <remove value="'"/>
389 <remove value="&quot;"/>
390 </valid>
391 </sanitizer>
392 </param>
393 <param name="param_tmt10plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) ">
394 <sanitizer>
395 <valid initial="string.printable">
396 <remove value="'"/>
397 <remove value="&quot;"/>
398 </valid>
399 </sanitizer>
400 </param>
401 <param name="param_tmt10plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) ">
402 <sanitizer>
403 <valid initial="string.printable">
404 <remove value="'"/>
405 <remove value="&quot;"/>
406 </valid>
407 </sanitizer>
408 </param>
409 <param name="param_tmt10plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) ">
410 <sanitizer>
411 <valid initial="string.printable">
412 <remove value="'"/>
413 <remove value="&quot;"/>
414 </valid>
415 </sanitizer>
416 </param>
417 <param name="param_tmt10plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) ">
418 <sanitizer>
419 <valid initial="string.printable">
420 <remove value="'"/>
421 <remove value="&quot;"/>
422 </valid>
423 </sanitizer>
424 </param>
425 <param name="param_tmt10plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) ">
426 <sanitizer>
427 <valid initial="string.printable">
428 <remove value="'"/>
429 <remove value="&quot;"/>
430 </valid>
431 </sanitizer>
432 </param>
433 <param name="param_tmt10plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) ">
434 <sanitizer>
435 <valid initial="string.printable">
436 <remove value="'"/>
437 <remove value="&quot;"/>
438 </valid>
439 </sanitizer>
440 </param>
441 <param name="param_tmt10plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) ">
442 <sanitizer>
443 <valid initial="string.printable">
444 <remove value="'"/>
445 <remove value="&quot;"/>
446 </valid>
447 </sanitizer>
448 </param>
449 <param name="param_tmt10plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="(-reference_channel) ">
450 <option value="126" selected="true">126</option>
451 <option value="127N">127N</option>
452 <option value="127C">127C</option>
453 <option value="128N">128N</option>
454 <option value="128C">128C</option>
455 <option value="129N">129N</option>
456 <option value="129C">129C</option>
457 <option value="130N">130N</option>
458 <option value="130C">130C</option>
459 <option value="131">131</option>
460 </param>
461 <repeat name="rep_param_tmt10plex_correction_matrix" min="0" max="1" title="param_tmt10plex_correction_matrix">
462 <param name="param_tmt10plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
463 <sanitizer>
464 <valid initial="string.printable">
465 <remove value="'"/>
466 <remove value="&quot;"/>
467 </valid>
468 </sanitizer>
469 </param>
470 </repeat>
471 <param name="param_tmt6plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
472 <sanitizer>
473 <valid initial="string.printable">
474 <remove value="'"/>
475 <remove value="&quot;"/>
476 </valid>
477 </sanitizer>
478 </param>
479 <param name="param_tmt6plex_channel_127_description" type="text" size="30" label="Description for the content of the 127 channel" help="(-channel_127_description) ">
480 <sanitizer>
481 <valid initial="string.printable">
482 <remove value="'"/>
483 <remove value="&quot;"/>
484 </valid>
485 </sanitizer>
486 </param>
487 <param name="param_tmt6plex_channel_128_description" type="text" size="30" label="Description for the content of the 128 channel" help="(-channel_128_description) ">
488 <sanitizer>
489 <valid initial="string.printable">
490 <remove value="'"/>
491 <remove value="&quot;"/>
492 </valid>
493 </sanitizer>
494 </param>
495 <param name="param_tmt6plex_channel_129_description" type="text" size="30" label="Description for the content of the 129 channel" help="(-channel_129_description) ">
496 <sanitizer>
497 <valid initial="string.printable">
498 <remove value="'"/>
499 <remove value="&quot;"/>
500 </valid>
501 </sanitizer>
502 </param>
503 <param name="param_tmt6plex_channel_130_description" type="text" size="30" label="Description for the content of the 130 channel" help="(-channel_130_description) ">
504 <sanitizer>
505 <valid initial="string.printable">
506 <remove value="'"/>
507 <remove value="&quot;"/>
508 </valid>
509 </sanitizer>
510 </param>
511 <param name="param_tmt6plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) ">
512 <sanitizer>
513 <valid initial="string.printable">
514 <remove value="'"/>
515 <remove value="&quot;"/>
516 </valid>
517 </sanitizer>
518 </param>
519 <param name="param_tmt6plex_reference_channel" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-reference_channel) "/>
520 <repeat name="rep_param_tmt6plex_correction_matrix" min="0" max="1" title="param_tmt6plex_correction_matrix">
521 <param name="param_tmt6plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
522 <sanitizer>
523 <valid initial="string.printable">
524 <remove value="'"/>
525 <remove value="&quot;"/>
526 </valid>
527 </sanitizer>
528 </param>
529 </repeat>
530 <expand macro="advanced_options">
531 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
532 <param name="param_extraction_precursor_isotope_deviation" type="float" min="0.0" optional="True" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help="(-precursor_isotope_deviation) "/>
533 <param name="param_extraction_purity_interpolation" display="radio" type="select" optional="False" value="true" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" help="(-purity_interpolation) If set to false, only the precursor scan will be used">
534 <option value="true" selected="true">true</option>
535 <option value="false">false</option>
536 </param>
537 </expand>
538 </inputs>
539 <outputs>
540 <data name="param_out" format="consensusxml"/>
541 </outputs>
542 <help>Calculates isobaric quantitative values for peptides
543
544
545 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html</help>
546 </tool>