Mercurial > repos > galaxyp > msconvert
comparison msconvert_macros.xml @ 0:ab59b1826345 draft
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 |
parents | |
children | 987d73278bf9 |
comparison
equal
deleted
inserted
replaced
-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 "known" 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 "Aggregated fraction" 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> |