0
+ − 1 <tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0">
+ − 2 <!-- BEGIN_VERSION_RAW -->
+ − 3 <description>Convert and filter a Thermo Finnigan RAW file</description>
+ − 4 <!-- END_VERSION_RAW -->
+ − 5 <!-- BEGIN_VERSION_DEFAULT -->
+ − 6 <description>Convert and filter a mass spec peak list</description>
+ − 7 <!-- END_VERSION_DEFAULT -->
+ − 8
+ − 9 <command interpreter="python">
+ − 10 msconvert_wrapper.py
+ − 11 --input=${input}
+ − 12 #if hasattr($input, 'display_name')
+ − 13 --input_name='${input.display_name}'
+ − 14 #end if
+ − 15 --output=${output}
+ − 16 ## BEGIN_VERSION_DEFAULT
+ − 17 --fromextension=${input.ext}
+ − 18 ## END_VERSION_DEFAULT
+ − 19
+ − 20 ## BEGIN_VERSION_RAW
+ − 21 --fromextension=RAW
+ − 22 ## END_VERSION_RAW
+ − 23
+ − 24 --toextension=${output_type}
+ − 25
+ − 26 #if $settings.settingsType == "full"
+ − 27 --binaryencoding=${settings.binary_encoding}
+ − 28 --mzencoding=${settings.mz_encoding}
+ − 29 --intensityencoding=${settings.intensity_encoding}
+ − 30 --zlib=${settings.zlib}
+ − 31 #end if
+ − 32
+ − 33 #if $filtering.filtering_use
+ − 34
+ − 35 #if $filtering.precursor_recalculation.value
+ − 36 --filter "precursorRecalculation"
+ − 37 #end if
+ − 38
+ − 39 #if $filtering.peak_picking.pick_peaks
+ − 40 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
+ − 41 #end if
+ − 42
+ − 43 #if str($filtering.activation) != "false"
+ − 44 --filter "activation $filtering.activation"
+ − 45 #end if
+ − 46
+ − 47 #if len($filtering.indices) > 0
+ − 48 --filter "index
+ − 49 #for $index in $filtering.indices
+ − 50 [${index.from},${index.to}]
+ − 51 #end for
+ − 52 "
+ − 53 #end if
+ − 54
+ − 55 #if len($filtering.scan_numbers) > 0
+ − 56 --filter "scanNumber
+ − 57 #for $scan_number in $filtering.scan_numbers
+ − 58 [${scan_number.from},${scan_number.to}]
+ − 59 #end for
+ − 60 "
+ − 61 #end if
+ − 62
+ − 63 #for threshold_entry in $filtering.threshold_repeat
+ − 64 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
+ − 65 #end for
+ − 66
+ − 67
+ − 68 #if $filtering.strip_it.value
+ − 69 --filter "stripIT"
+ − 70 #end if
+ − 71
+ − 72 #if $filtering.filter_mz_windows.do_filter
+ − 73 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
+ − 74 #end if
+ − 75
+ − 76
+ − 77 #if $filtering.filter_ms_levels.do_filter
+ − 78 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
+ − 79 #end if
+ − 80
+ − 81 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
+ − 82 --filter "ETDFilter"
+ − 83 #end if
+ − 84
+ − 85 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
+ − 86 --filter "ETDFilter removePrecursor:$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"
+ − 87 #end if
+ − 88
+ − 89 ## BEGIN_VERSION_3
+ − 90
+ − 91 #if $filtering.precursor_refine.value
+ − 92 --filter "precursorRefine"
+ − 93 #end if
+ − 94
+ − 95 #if $filtering.ms2denoise.denoise
+ − 96 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
+ − 97 #end if
+ − 98
+ − 99 #if str($filtering.ms2deisotope) == "true"
+ − 100 --filter "MS2Deisotope"
+ − 101 #end if
+ − 102
+ − 103 #if str($filtering.polarity) != "false"
+ − 104 --filter "polarity $filtering.polarity"
+ − 105 #end if
+ − 106
+ − 107 #if str($filtering.analyzer) != "false"
+ − 108 --filter "analyzer $filtering.analyzer"
+ − 109 #end if
+ − 110
+ − 111 ## END_VERSION_3
+ − 112
+ − 113 #end if
+ − 114
+ − 115 </command>
+ − 116
+ − 117 <inputs>
+ − 118 <!-- BEGIN_VERSION_RAW -->
+ − 119 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
+ − 120 <!-- END_VERSION_RAW -->
+ − 121
+ − 122 <!-- BEGIN_VERSION_DEFAULT -->
+ − 123 <conditional name="type">
+ − 124 <param name="input_type" type="select" label="Input Type">
+ − 125 <option value="mzml">mzML</option>
+ − 126 <option value="mzxml">mzXML</option>
+ − 127 <option value="mgf">mgf</option>
+ − 128 <option value="ms2">ms2</option>
+ − 129 </param>
+ − 130 <when value="mzml">
+ − 131 <param format="mzml" name="input" type="data" label="Input mzML"/>
+ − 132 </when>
+ − 133 <when value="mzxml">
+ − 134 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+ − 135 </when>
+ − 136 <when value="mgf">
+ − 137 <param format="mgf" name="input" type="data" label="Input mgf"/>
+ − 138 </when>
+ − 139 <when value="ms2">
+ − 140 <param format="ms2" name="input" type="data" label="Input ms2"/>
+ − 141 </when>
+ − 142 </conditional>
+ − 143 <!-- END_VERSION_DEFAULT -->
+ − 144 <param name="output_type" type="select" label="Output Type">
+ − 145 <option value="mzML">mzML (indexed)</option>
+ − 146 <option value="unindexed_mzML">mzML (unindexed)</option>
+ − 147 <option value="mzXML">mzXML (indexed)</option>
+ − 148 <option value="unindexed_mzXML">mzXML (unindexed)</option>
+ − 149 <option value="mgf">mgf</option>
+ − 150 <option value="ms2">ms2</option>
+ − 151 </param>
+ − 152 <conditional name="filtering">
+ − 153 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
+ − 154 <when value="false" />
+ − 155 <when value="true">
+ − 156 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
+ − 157 <!-- BEGIN_VERSION_3 -->
+ − 158 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
+ − 159 <!-- END_VERSION_3 -->
+ − 160
+ − 161
+ − 162 <conditional name="peak_picking">
+ − 163 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
+ − 164 <when value="false" />
+ − 165 <when value="true">
+ − 166 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
+ − 167 <option value="1">MS1 Only (1)</option>
+ − 168 <option value="2">MS2 Only (2)</option>
+ − 169 <option value="2-">MS2 and on (2-)</option>
+ − 170 <option value="1-">All Levels (1-)</option>
+ − 171 </param>
+ − 172 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
+ − 173 </when>
+ − 174 </conditional>
+ − 175
+ − 176 <repeat name="threshold_repeat" title="Filter by Threshold">
+ − 177 <conditional name="threshold">
+ − 178 <param type="select" label="Specify threshold on" name="threshold_type" help="">
+ − 179 <option value="count">Peak count</option>
+ − 180 <option value="count-after-ties">Peak count (after ties)</option>
+ − 181 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
+ − 182 <option value="bpi-relative">Percent of base peak intensity</option>
+ − 183 <option value="tic-relative">Percent of total ion current</option>
+ − 184 <option value="tic-fraction">Aggregate percent of total ion current</option>
+ − 185 </param>
+ − 186 <when value="count">
+ − 187 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
+ − 188 </when>
+ − 189 <when value="count-after-ties">
+ − 190 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
+ − 191 </when>
+ − 192 <when value="absolute">
+ − 193 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
+ − 194 </when>
+ − 195 <when value="bpi-relative">
+ − 196 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
+ − 197 />
+ − 198 </when>
+ − 199 <when value="tic-relative">
+ − 200 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
+ − 201 />
+ − 202 </when>
+ − 203 <when value="tic-fraction">
+ − 204 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
+ − 205 </when>
+ − 206 </conditional>
+ − 207 <param type="select" label="Keep" name="orientation">
+ − 208 <option value="most-intense">Most intense peaks</option>
+ − 209 <option value="least-intense">Least intense peaks</option>
+ − 210 </param>
+ − 211 </repeat>
+ − 212
+ − 213
+ − 214 <param name="activation" type="select" label="Filter by Activation">
+ − 215 <option value="false" selected="true">no</option>
+ − 216 <option value="ETD">ETD</option>
+ − 217 <option value="CID">CID</option>
+ − 218 <option value="SA">SA</option>
+ − 219 <option value="HCD">HCD</option>
+ − 220 <!-- BEGIN_VERSION_3 -->
+ − 221 <option>BIRD</option>
+ − 222 <option>ECD</option>
+ − 223 <option>IRMPD</option>
+ − 224 <option>PD</option>
+ − 225 <option>PSD</option>
+ − 226 <option>PQD</option>
+ − 227 <option>SID</option>
+ − 228 <option>SORI</option>
+ − 229 <!-- END_VERSION_3 -->
+ − 230 </param>
+ − 231
+ − 232 <repeat name="indices" title="Filter Scan Indices">
+ − 233 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
+ − 234 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
+ − 235 </repeat>
+ − 236
+ − 237 <repeat name="scan_numbers" title="Filter Scan Numbers">
+ − 238 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
+ − 239 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
+ − 240 </repeat>
+ − 241
+ − 242 <conditional name="filter_mz_windows">
+ − 243 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+ − 244 <when value="false" />
+ − 245 <when value="true">
+ − 246 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
+ − 247 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
+ − 248 </when>
+ − 249 </conditional>
+ − 250
+ − 251 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
+ − 252
+ − 253 <conditional name="filter_ms_levels">
+ − 254 <param name="do_filter" type="boolean" label="Filter MS Levels" />
+ − 255 <when value="false" />
+ − 256 <when value="true">
+ − 257 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
+ − 258 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
+ − 259 </when>
+ − 260 </conditional>
+ − 261
+ − 262 <conditional name="etd_filtering">
+ − 263 <param name="do_etd_filtering" type="select" label="ETD Filtering">
+ − 264 <option value="none" selected="true">none</option>
+ − 265 <option value="default">yes (with default options)</option>
+ − 266 <option value="advanced">yes (show advanced options) </option>
+ − 267 </param>
+ − 268 <when value="none" />
+ − 269 <when value="default" />
+ − 270 <when value="advanced">
+ − 271 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
+ − 272 </param>
+ − 273 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
+ − 274 <option value="MZ" selected="true">mz</option>
+ − 275 <option value="PPM">ppm</option>
+ − 276 </param>
+ − 277 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
+ − 278 <option value="true" selected="true">yes</option>
+ − 279 <option value="false">no</option>
+ − 280 </param>
+ − 281 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
+ − 282 <option value="true" selected="true">yes</option>
+ − 283 <option value="false">no</option>
+ − 284 </param>
+ − 285 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
+ − 286 <option value="true" selected="true">yes</option>
+ − 287 <option value="false">no</option>
+ − 288 </param>
+ − 289 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
+ − 290 <option value="true" selected="true">yes</option>
+ − 291 <option value="false">no</option>
+ − 292 </param>
+ − 293 </when>
+ − 294 </conditional>
+ − 295
+ − 296
+ − 297 <!-- BEGIN_VERSION_3 -->
+ − 298 <conditional name="ms2denoise">
+ − 299 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
+ − 300 <when value="true">
+ − 301 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
+ − 302 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
+ − 303 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
+ − 304 </when>
+ − 305 <when value="false" />
+ − 306 </conditional>
+ − 307 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
+ − 308
+ − 309 <param name="polarity" type="select" label="Filter by Polarity">
+ − 310 <option value="false" selected="true">no</option>
+ − 311 <option value="positive">positive</option>
+ − 312 <option value="negative">negative</option>
+ − 313 </param>
+ − 314
+ − 315 <param name="analyzer" type="select" label="Filter by Analyzer">
+ − 316 <option value="false" selected="true">no</option>
+ − 317 <option value="quad">quad</option>
+ − 318 <option value="orbi">orbi</option>
+ − 319 <option value="FT">FT</option>
+ − 320 <option value="IT">IT</option>
+ − 321 <option value="TOF">TOF</option>
+ − 322 </param>
+ − 323 <!-- END_VERSION_3 -->
+ − 324 </when>
+ − 325 </conditional>
+ − 326
+ − 327 <conditional name="settings">
+ − 328 <param name="settingsType" type="select" label="Advanced Settings" help="">
+ − 329 <option value="default">Use Defaults</option>
+ − 330 <option value="full">Full Parameter List</option>
+ − 331 </param>
+ − 332 <when value="default" />
+ − 333 <when value="full">
+ − 334 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
+ − 335 <option value="64" selected="true">64</option>
+ − 336 <option value="32">32</option>
+ − 337 </param>
+ − 338 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
+ − 339 <option value="64" selected="true">64</option>
+ − 340 <option value="32">32</option>
+ − 341 </param>
+ − 342 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
+ − 343 <option value="64">64</option>
+ − 344 <option value="32" selected="true">32</option>
+ − 345 </param>
+ − 346 <param type="boolean" name="zlib" label="Use zlib">
+ − 347 </param>
+ − 348 </when>
+ − 349 </conditional>
+ − 350
+ − 351
+ − 352 </inputs>
+ − 353 <outputs>
+ − 354 <data format="mzml" name="output">
+ − 355 <change_format>
+ − 356 <when input="output_type" value="mzXML" format="mzxml" />
+ − 357 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
+ − 358 <when input="output_type" value="ms2" format="ms2" />
+ − 359 <when input="output_type" value="mgf" format="mgf" />
+ − 360 </change_format>
+ − 361 </data>
+ − 362 </outputs>
+ − 363
+ − 364 <requirements>
+ − 365 <requirement type="package">proteowizard</requirement>
+ − 366 </requirements>
+ − 367
+ − 368 <help>
+ − 369 **What it does**
+ − 370
+ − 371 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
+ − 372
+ − 373 You can view the original documentation here_.
+ − 374
+ − 375 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
+ − 376
+ − 377 ------
+ − 378
+ − 379 **Citation**
+ − 380
+ − 381 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.`
+ − 382
+ − 383 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
+ − 384
+ − 385 </help>
+ − 386 </tool>