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comparison msconvert_macros.xml @ 0:ab59b1826345 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
author galaxyp
date Thu, 22 Oct 2015 14:00:58 -0400
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children 987d73278bf9
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-1:000000000000 0:ab59b1826345
1 <macros>
2 <xml name="msconvertCommand">
3 <command>
4 <![CDATA[
5 #import re
6 #set $output_type_str = str($output_type)
7 #set $input_name = $input.display_name
8 #set $output_name = $input_name.split(".")[0] + "." + $output_type_str
9 ln -s '$input' '${input_name}' &&
10
11 #if $data_processing.precursor_refinement.use_mzrefinement
12 #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name
13 ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_name}' &&
14 #end if
15
16 mkdir outdir &&
17 msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name'
18
19 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
20 #if $data_processing.peak_picking.pick_peaks
21 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
22 #end if
23
24 #if $data_processing.precursor_refinement.use_mzrefinement
25 --filter "mzRefiner $input_ident_name
26 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
27 thresholdScore=$data_processing.precursor_refinement.thresholdScore
28 thresholdValue=$data_processing.precursor_refinement.thresholdValue
29 thresholdStep=$data_processing.precursor_refinement.thresholdStep
30 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
31 #end if
32
33 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
34 --filter "chargeStatePredictor
35 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
36 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
37 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
38 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
39 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
40 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
41 --filter "turbocharger
42 minCharge=$data_processing.charge_state_calculation.minCharge
43 maxCharge=$data_processing.charge_state_calculation.maxCharge
44 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
45 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
46 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
47 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
48 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
49 #end if
50
51 #for threshold_entry in $data_processing.thresholds
52 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
53 #end for
54
55 #if $data_processing.filter_mz_windows.do_mzwindow_filter
56 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
57 #end if
58
59 #if $data_processing.etd_filtering.do_etd_filtering
60 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
61 $data_processing.etd_filtering.remove_charge_reduced
62 $data_processing.etd_filtering.remove_neutral_loss
63 $data_processing.etd_filtering.blanket_removal
64 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
65 #end if
66
67 #if $data_processing.ms2denoise.denoise
68 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
69 #end if
70
71 #if str($data_processing.ms2deisotope) == "true"
72 --filter "MS2Deisotope"
73 #end if
74
75
76 ## SCAN INCLUSION/EXCLUSION FILTERS
77 #if str($filtering.activation) != "false"
78 --filter "activation $filtering.activation"
79 #end if
80
81 #if len($filtering.indices) > 0
82 --filter "index
83 #for $index in $filtering.indices
84 [${index.from},${index.to}]
85 #end for
86 "
87 #end if
88
89 #if len($filtering.scan_numbers) > 0
90 --filter "scanNumber
91 #for $scan_number in $filtering.scan_numbers
92 [${scan_number.from},${scan_number.to}]
93 #end for
94 "
95 #end if
96
97 #if $filtering.strip_it.value
98 --filter "stripIT"
99 #end if
100
101 #if $filtering.filter_ms_levels.do_ms_level_filter
102 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
103 #end if
104
105 #if str($filtering.polarity) != "false"
106 --filter "polarity $filtering.polarity"
107 #end if
108
109 #if str($filtering.analyzer) != "false"
110 --filter "analyzer $filtering.analyzer"
111 #end if
112
113 ## OUTPUT ENCODING
114 #set $mz_encoding = str($settings.mz_encoding)
115 #set $intensity_encoding = str($settings.intensity_encoding)
116 #if $mz_encoding == $intensity_encoding
117 #if $mz_encoding == "64"
118 --64
119 #else
120 --32
121 #end if
122 #else
123 --mz${mz_encoding}
124 --inten${intensity_encoding}
125 #end if
126
127 #set binary_compression = str($settings.binary_compression)
128 #if $binary_compression == "zlib"
129 --zlib
130 #else if $binary_compression == "numpressLinearPic"
131 --numpressLinear --numpressPic
132 #else if $binary_compression == "numpressLinearSlof"
133 --numpressLinear --numpressSlof
134 #else if $binary_compression == "numpressLinear"
135 --numpressLinear
136 #else if $binary_compression == "numpressPic"
137 --numpressPic
138 #else if $binary_compression == "numpressSlof"
139 --numpressSlof
140 #end if
141
142 #if $settings.gzip_compression
143 --gzip
144 #end if
145
146 &&
147
148 #if $data_processing.precursor_refinement.use_mzrefinement
149 mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
150 #end if
151
152 mv 'outdir/$output_name' output &&
153 rmdir outdir
154 ]]>
155 </command>
156 </xml>
157
158 <xml name="msconvertInputParameters">
159 <param name="output_type" type="select" label="Output Type">
160 <option value="mz5" selected="true">mz5</option>
161 <option value="mzML">mzML</option>
162 <option value="mzXML">mzXML</option>
163 <option value="mgf">mgf</option>
164 <option value="ms2">ms2</option>
165 </param>
166
167 <section name="data_processing" title="Data Processing Filters">
168
169 <conditional name="peak_picking">
170 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
171 <when value="false" />
172 <when value="true">
173 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
174 <option value="1">MS1 Only (1)</option>
175 <option value="2">MS2 Only (2)</option>
176 <option value="2-">MS2 and on (2-)</option>
177 <option value="1-" selected="true">All Levels (1-)</option>
178 </param>
179 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
180 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
181 <option value="cwt">CantWaiT - continuous wavelet transform</option>
182 </param>
183 </when>
184 </conditional>
185
186 <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true">
187 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
188 <when value="false"></when>
189 <when value="true">
190 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
191 <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+" />
192 <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." />
193 <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
194 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
195 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
196 <option value="1">MS1 Only (1)</option>
197 <option value="2">MS2 Only (2)</option>
198 <option value="2-">MS2 and on (2-)</option>
199 <option value="1-" selected="true">All Levels (1-)</option>
200 </param>
201 </when>
202 </conditional>
203
204 <conditional name="charge_state_calculation">
205 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
206 <option value="false">no</option>
207 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
208 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
209 </param>
210 <when value="false" />
211 <when value="predictor">
212 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
213 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
214 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
215 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
216 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
217 </when>
218 <when value="turbocharger">
219 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
220 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
221 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
222 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
223 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
224 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
225 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
226 </when>
227 </conditional>
228
229 <repeat name="thresholds" title="Filter by Threshold">
230 <param type="select" label="Specify threshold on" name="threshold_type" help="">
231 <option value="count">Peak count</option>
232 <option value="count-after-ties">Peak count (after ties)</option>
233 <option value="absolute">Peak absolute intensity</option>
234 <option value="bpi-relative">Fraction of base peak intensity</option>
235 <option value="tic-relative">Fraction of total ion current</option>
236 <option value="tic-fraction">Aggregate fraction of total ion current</option>
237 </param>
238 <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
239 <param type="select" label="Keep" name="orientation">
240 <option value="most-intense">Most intense peaks</option>
241 <option value="least-intense">Least intense peaks</option>
242 </param>
243 </repeat>
244
245 <conditional name="filter_mz_windows">
246 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
247 <when value="false" />
248 <when value="true">
249 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
250 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
251 </when>
252 </conditional>
253
254 <conditional name="etd_filtering">
255 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
256 <when value="false" />
257 <when value="true">
258 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
259 <option value="true" selected="true">yes</option>
260 <option value="false">no</option>
261 </param>
262 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
263 <option value="true" selected="true">yes</option>
264 <option value="false">no</option>
265 </param>
266 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
267 <option value="true" selected="true">yes</option>
268 <option value="false">no</option>
269 </param>
270 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
271 <option value="true" selected="true">yes</option>
272 <option value="false">no</option>
273 </param>
274 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
275 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
276 <option value="MZ" selected="true">mz</option>
277 <option value="PPM">ppm</option>
278 </param>
279 </when>
280 </conditional>
281
282 <conditional name="ms2denoise">
283 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
284 <when value="true">
285 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
286 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
287 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
288 </when>
289 <when value="false" />
290 </conditional>
291
292 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
293
294 </section>
295
296
297 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
298
299 <param name="activation" type="select" label="Filter by Activation">
300 <option value="false" selected="true">no</option>
301 <option value="ETD">ETD</option>
302 <option value="CID">CID</option>
303 <option value="SA">SA</option>
304 <option value="HCD">HCD</option>
305 <option>BIRD</option>
306 <option>ECD</option>
307 <option>IRMPD</option>
308 <option>PD</option>
309 <option>PSD</option>
310 <option>PQD</option>
311 <option>SID</option>
312 <option>SORI</option>
313 </param>
314
315 <repeat name="indices" title="Filter Scan Indices">
316 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
317 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
318 </repeat>
319
320 <repeat name="scan_numbers" title="Filter Scan Numbers">
321 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
322 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
323 </repeat>
324
325 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
326
327 <conditional name="filter_ms_levels">
328 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
329 <when value="false" />
330 <when value="true">
331 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
332 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
333 </when>
334 </conditional>
335
336 <param name="polarity" type="select" label="Filter by Polarity">
337 <option value="false" selected="true">no</option>
338 <option value="positive">positive</option>
339 <option value="negative">negative</option>
340 </param>
341
342 <param name="analyzer" type="select" label="Filter by Analyzer">
343 <option value="false" selected="true">no</option>
344 <option value="quad">Quadrupole</option>
345 <option value="orbi">Orbitrap</option>
346 <option value="FT">Fourier-transform</option>
347 <option value="IT">Ion trap</option>
348 <option value="TOF">Time of flight</option>
349 </param>
350 </section>
351
352
353 <section name="settings" title="Output Encoding Settings">
354 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
355 <option value="64" selected="true">64</option>
356 <option value="32">32</option>
357 </param>
358 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
359 <option value="64">64</option>
360 <option value="32" selected="true">32</option>
361 </param>
362 <param type="select" name="binary_compression" label="Binary data compression">
363 <option value="false">None</option>
364 <option value="zlib" selected="true">zlib</option>
365 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
366 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
367 <option value="numpressLinear">numpressLinear only</option>
368 <option value="numpressPic">numpressPic only</option>
369 <option value="numpressSlof">numpressSlof only</option>
370 </param>
371 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
372 </section>
373 </xml>
374
375 <xml name="msconvertOutput">
376 <outputs>
377 <data format="mzml" name="output" from_work_dir="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
378 <change_format>
379 <when input="output_type" value="mz5" format="mz5" />
380 <when input="output_type" value="mzXML" format="mzxml" />
381 <when input="output_type" value="ms2" format="ms2" />
382 <when input="output_type" value="mgf" format="mgf" />
383 </change_format>
384 </data>
385 <data format="csv" name="output.refinement" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
386
387 </data>
388 </outputs>
389 </xml>
390 </macros>