Mercurial > repos > galaxyp > msconvert
comparison msconvert3_raw.xml @ 4:001e77708ec9
Uploaded
author | galaxyp |
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date | Fri, 12 Jul 2013 12:45:51 -0400 |
parents | 7e41529ee90c |
children | 08bb52273ae1 |
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3:7e41529ee90c | 4:001e77708ec9 |
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112 | 112 |
113 </command> | 113 </command> |
114 | 114 |
115 <inputs> | 115 <inputs> |
116 <!-- BEGIN_VERSION_RAW --> | 116 <!-- BEGIN_VERSION_RAW --> |
117 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> | 117 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> |
118 <!-- END_VERSION_RAW --> | 118 <!-- END_VERSION_RAW --> |
119 | 119 |
120 <param name="output_type" type="select" label="Output Type"> | 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)"> |
121 <option value="mzML">mzML (indexed)</option> | 121 <option value="mzML">mzML (indexed)</option> |
122 <option value="unindexed_mzML">mzML (unindexed)</option> | 122 <option value="unindexed_mzML">mzML (unindexed)</option> |
123 <option value="mzXML">mzXML (indexed)</option> | 123 <option value="mzXML">mzXML (indexed)</option> |
124 <option value="unindexed_mzXML">mzXML (unindexed)</option> | 124 <option value="unindexed_mzXML">mzXML (unindexed)</option> |
125 <option value="mgf">mgf</option> | 125 <option value="mgf">mgf</option> |
126 <option value="ms2">ms2</option> | 126 <option value="ms2">ms2</option> |
127 </param> | 127 </param> |
128 <conditional name="filtering"> | 128 <conditional name="filtering"> |
129 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> | 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)" /> |
130 <when value="false" /> | 130 <when value="false" /> |
131 <when value="true"> | 131 <when value="true"> |
132 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> | 132 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> |
133 <!-- BEGIN_VERSION_3 --> | 133 <!-- BEGIN_VERSION_3 --> |
134 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> | 134 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> |
351 | 351 |
352 You can view the original documentation here_. | 352 You can view the original documentation here_. |
353 | 353 |
354 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | 354 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html |
355 | 355 |
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) | |
356 ------ | 371 ------ |
357 | 372 |
358 **Citation** | 373 **Citation** |
359 | 374 |
360 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.` | 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.` |