Mercurial > repos > galaxyp > msconvert
annotate msconvert.xml @ 9:dd4ba10d0c45 draft
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
| author | galaxyp |
|---|---|
| date | Wed, 07 Dec 2016 16:43:07 -0500 |
| parents | d2c61663e33c |
| children | 9d5de24e6ef7 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="msconvert" name="msconvert" version="0.3.0"> |
| 2 <!-- BEGIN_VERSION_DEFAULT --> | |
| 3 <description>Convert and filter a mass spec peak list</description> | |
| 4 <!-- END_VERSION_DEFAULT --> | |
| 5 <!-- | |
| 6 <requirements> | |
| 7 <requirement type="package" version="3_0_4388">proteowizard</requirement> | |
| 8 </requirements> | |
| 9 --> | |
| 10 <command interpreter="python"> | |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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11 #import re |
| 8 | 12 #set $ext = $input.ext |
| 13 msconvert_wrapper.py | |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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14 #if $type.input_type == 'wiff': |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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15 #set basename = 'absciex' |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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16 #if hasattr($input, 'display_name') |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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17 #set basename = $re.sub('\W','_',$input.display_name) |
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18 #end if |
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19 --input=${input.extra_files_path}/wiff |
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20 --input_name='${basename}.wiff |
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21 --implicit=${input.extra_files_path}/wiff_scan |
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22 --input=${input.extra_files_path}/wiff_scan |
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23 --input_name='${basename}.wiff.scan |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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24 #else |
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25 --input=${input} |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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26 #if hasattr($input, 'display_name') |
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27 --input_name='${input.display_name}' |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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28 #end if |
| 8 | 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> | |
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138 <option value="wiff">wiff</option> |
| 8 | 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> | |
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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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changeset
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152 <when value="wiff"> |
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153 <param format="wiff" name="input" type="data" label="Input wiff"/> |
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154 </when> |
| 8 | 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 | |
| 365 </inputs> | |
| 366 <outputs> | |
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367 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > |
| 8 | 368 <change_format> |
| 369 <when input="output_type" value="mzXML" format="mzxml" /> | |
| 370 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> | |
| 371 <when input="output_type" value="ms2" format="ms2" /> | |
| 372 <when input="output_type" value="mgf" format="mgf" /> | |
| 373 </change_format> | |
| 374 </data> | |
| 375 </outputs> | |
| 376 <help> | |
| 377 **What it does** | |
| 378 | |
| 379 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. | |
| 380 | |
| 381 You can view the original documentation here_. | |
| 382 | |
| 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. https://bitbucket.org/galaxyp/msconvert | |
| 392 | |
| 393 </help> | |
| 394 </tool> |