Mercurial > repos > galaxyp > msconvert
diff 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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--- a/msconvert3_raw.xml Thu Jun 20 16:08:23 2013 -0400 +++ b/msconvert3_raw.xml Fri Jul 12 12:45:51 2013 -0400 @@ -114,10 +114,10 @@ <inputs> <!-- BEGIN_VERSION_RAW --> - <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> + <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> <!-- END_VERSION_RAW --> - <param name="output_type" type="select" label="Output Type"> + <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)"> <option value="mzML">mzML (indexed)</option> <option value="unindexed_mzML">mzML (unindexed)</option> <option value="mzXML">mzXML (indexed)</option> @@ -126,7 +126,7 @@ <option value="ms2">ms2</option> </param> <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <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)" /> <when value="false" /> <when value="true"> <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> @@ -353,6 +353,21 @@ .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html +**Recommended** + +For X!tandem searches: Use mzml format generated from RAW file. + + RAW → mzml + +For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter. + + RAW → mzml → MGF (ProteinPilot) + +For MaxQuant searches: Use RAW file as an input. + +For OMSSA : Use MGF format generated from mzml file using MGF formatter. + + RAW → mzml → MGF (Mascot) ------ **Citation**