Mercurial > repos > galaxyp > msconvert
comparison msconvert3_raw.xml @ 5:08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 17 Feb 2014 08:13:33 -0600 |
parents | 001e77708ec9 |
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4:001e77708ec9 | 5:08bb52273ae1 |
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1 <tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.0"> | 1 <tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.1"> |
2 <!-- BEGIN_VERSION_RAW --> | 2 <!-- BEGIN_VERSION_RAW --> |
3 <description>Convert and filter a Thermo Finnigan RAW file</description> | 3 <description>Convert and filter a Thermo Finnigan RAW file</description> |
4 <!-- END_VERSION_RAW --> | 4 <!-- END_VERSION_RAW --> |
5 | 5 <requirements> |
6 <requirement type="package">proteowizard</requirement> | |
7 <!-- BEGIN_VERSION_RAW --> | |
8 <requirement type="platform">windows</requirement> | |
9 <!-- END_VERSION_RAW --> | |
10 </requirements> | |
6 <command interpreter="python"> | 11 <command interpreter="python"> |
7 #set $ext = $input.ext | 12 #set $ext = $input.ext |
8 #if $ext.startswith("m:") | 13 #if $ext.startswith("m:") |
9 #set $ext = $ext[len("m:"):] | 14 #set $ext = $ext[len("m:"):] |
10 #end if | 15 #end if |
115 <inputs> | 120 <inputs> |
116 <!-- BEGIN_VERSION_RAW --> | 121 <!-- BEGIN_VERSION_RAW --> |
117 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> | 122 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> |
118 <!-- END_VERSION_RAW --> | 123 <!-- END_VERSION_RAW --> |
119 | 124 |
120 <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is the standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)"> | 125 <param name="output_type" type="select" label="Output Type"> |
121 <option value="mzML">mzML (indexed)</option> | 126 <option value="mzML">mzML (indexed)</option> |
122 <option value="unindexed_mzML">mzML (unindexed)</option> | 127 <option value="unindexed_mzML">mzML (unindexed)</option> |
123 <option value="mzXML">mzXML (indexed)</option> | 128 <option value="mzXML">mzXML (indexed)</option> |
124 <option value="unindexed_mzXML">mzXML (unindexed)</option> | 129 <option value="unindexed_mzXML">mzXML (unindexed)</option> |
125 <option value="mgf">mgf</option> | 130 <option value="mgf">mgf</option> |
126 <option value="ms2">ms2</option> | 131 <option value="ms2">ms2</option> |
127 </param> | 132 </param> |
128 <conditional name="filtering"> | 133 <conditional name="filtering"> |
129 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (also called as peaklist processing)" /> | 134 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> |
130 <when value="false" /> | 135 <when value="false" /> |
131 <when value="true"> | 136 <when value="true"> |
132 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> | 137 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> |
133 <!-- BEGIN_VERSION_3 --> | 138 <!-- BEGIN_VERSION_3 --> |
134 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> | 139 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> |
334 <when input="output_type" value="ms2" format="ms2" /> | 339 <when input="output_type" value="ms2" format="ms2" /> |
335 <when input="output_type" value="mgf" format="mgf" /> | 340 <when input="output_type" value="mgf" format="mgf" /> |
336 </change_format> | 341 </change_format> |
337 </data> | 342 </data> |
338 </outputs> | 343 </outputs> |
339 | |
340 <requirements> | |
341 <requirement type="package">proteowizard</requirement> | |
342 <!-- BEGIN_VERSION_RAW --> | |
343 <requirement type="platform">windows</requirement> | |
344 <!-- END_VERSION_RAW --> | |
345 </requirements> | |
346 | |
347 <help> | 344 <help> |
348 **What it does** | 345 **What it does** |
349 | 346 |
350 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. | 347 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. |
351 | 348 |
352 You can view the original documentation here_. | 349 You can view the original documentation here_. |
353 | 350 |
354 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | 351 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html |
355 | 352 |
356 **Recommended** | |
357 | |
358 For X!tandem searches: Use mzml format generated from RAW file. | |
359 | |
360 RAW → mzml | |
361 | |
362 For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter. | |
363 | |
364 RAW → mzml → MGF (ProteinPilot) | |
365 | |
366 For MaxQuant searches: Use RAW file as an input. | |
367 | |
368 For OMSSA : Use MGF format generated from mzml file using MGF formatter. | |
369 | |
370 RAW → mzml → MGF (Mascot) | |
371 ------ | 353 ------ |
372 | 354 |
373 **Citation** | 355 **Citation** |
374 | 356 |
375 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.` | 357 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.` |