[proteowizard-commit] SF.net SVN: proteowizard:[4449] trunk

[<pcb...@us...>]

Revision: 4449
          http://sourceforge.net/p/proteowizard/code/4449
Author:   pcbrefugee
Date:     2013-03-28 20:51:00 +0000 (Thu, 28 Mar 2013)
Log Message:
-----------
[msconvert] correct the "act like ReAdW" web help example to do centroiding on all mslevels, and add it to the examples shown in commandline help

Modified Paths:
--------------
    trunk/pwiz/pwiz_tools/commandline/msconvert.cpp
    trunk/web/tools/msconvert.html

Modified: trunk/pwiz/pwiz_tools/commandline/msconvert.cpp
===================================================================
--- trunk/pwiz/pwiz_tools/commandline/msconvert.cpp	2013-03-28 12:38:45 UTC (rev 4448)
+++ trunk/pwiz/pwiz_tools/commandline/msconvert.cpp	2013-03-28 20:51:00 UTC (rev 4449)
@@ -309,6 +309,9 @@
           << "# put output file in my_output_dir\n"
           << "msconvert data.RAW -o my_output_dir\n"
           << endl
+          << "# combining options to create a smaller mzML file, much like the old ReAdW converter program\n"
+          << "msconvert data.RAW --32 --zlib --filter \"peakPicking true 1-\" --filter \"zeroSamples removeExtra\"\n"
+          << endl
           << "# extract scan indices 5...10 and 20...25\n"
           << "msconvert data.RAW --filter \"index [5,10] [20,25]\"\n"
           << endl

Modified: trunk/web/tools/msconvert.html
===================================================================
--- trunk/web/tools/msconvert.html	2013-03-28 12:38:45 UTC (rev 4448)
+++ trunk/web/tools/msconvert.html	2013-03-28 20:51:00 UTC (rev 4449)
@@ -19,7 +19,7 @@
         <p>
         Examples:
         <ul>
-		
+
             <li><code>msconvert</code><br/>
             (prints usage information)<p/></li>
 
@@ -40,13 +40,13 @@
 
             <li><code>msconvert data.RAW --filter "msLevel 2-"</code><br/>
             (only write ms2 and higher scans)<p/></li>
-			
-			<li><code>msconvert data.RAW  --filter "zeroSamples removeExtra"</code><br/>
+
+            <li><code>msconvert data.RAW  --filter "zeroSamples removeExtra"</code><br/>
             (omit zero-valued samples that are not next to non-zero samples)<p/></li>
 
-			<li><code>msconvert data.RAW --32 --zlib --filter "peakPicking true [2,3]" --filter "zeroSamples removeExtra" </code><br/>
+            <li><code>msconvert data.RAW --32 --zlib --filter "peakPicking true 1-" --filter "zeroSamples removeExtra" </code><br/>
             (various tricks to create a smaller file, much like the old ReAdW converter program)<p/></li>
-			
+
         </ul>
         </p>
     </p>

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