[Sashimi-commit] SF.net SVN: sashimi:[5437] branches/4-5/trans_proteomic_pipeline/CGI/ tpp_gui/tpp_gui.pl

[<rea...@us...>]

Revision: 5437
          http://sashimi.svn.sourceforge.net/sashimi/?rev=5437&view=rev
Author:   real_procopio
Date:     2011-06-21 01:23:15 +0000 (Tue, 21 Jun 2011)

Log Message:
-----------
[Petunia] Pass correct centroiding filter to msconvert; allow msconvert to convert wiff files, .d and .raw directories to mzML

Modified Paths:
--------------
    branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

Modified: branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl
===================================================================
--- branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl	2011-06-17 18:44:08 UTC (rev 5436)
+++ branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl	2011-06-21 01:23:15 UTC (rev 5437)
@@ -518,7 +518,7 @@
 	&addFiles(ref_page => 'rawfile',
 		  files    => [$rawfile]);
 
-	$page = 'mzxml';
+	$page = param('refpage') ? param('refpage') : 'mzxml';
 
     } elsif ( $action eq $web_actions{'switchPipeline'} ) {
 	# re-use addFiles, with a small hack
@@ -3177,28 +3177,31 @@
 	my $options = '-v --mzML'; # always verbose and mzML output
 	$options .= " -o $fdir";
 
-	$options .= ' -c [1,2]' if (param('msconvert_centroid'));
 	$options .= ' -z' if (param('msconvert_zlib'));
 	$options .= ' -g' if (param('msconvert_gzip'));
-
+	$options .= ' --filter "peakPicking true [1,2]"' if (param('msconvert_centroid'));
 	$options .= ' '.param('msconvert_extraopts') if (param('msconvert_extraopts'));
 
+	if ($in_cygwin) {
+	    chomp(my $w_file_path = `$command{cygpath} -w $file`);
+	    $command = "$command{msconvert} \"$w_file_path\" $options ";
+	} else {
+	    $command = "$command{msconvert} $file $options";
+	}
+
+	$out_file = $file; # modified below
 	if ($file =~ /raw$/i) {
-
-	    if ($in_cygwin) {
-		chomp(my $w_file_path = `$command{cygpath} -w $file`);
-		$command = "$command{msconvert} $options \"$w_file_path\" ";
-	    } else {
-		$command = "$command{msconvert} $options $file";
-	    }
-	    $out_file = $file;
 	    $out_file =~ s/\.raw$/\.mzML/i;
-
+	} elsif ($file =~ /wiff$/i) {
+	    $out_file =~ s/\.wiff$/\.mzML/i;
+	} elsif ($file =~ /\.d$/i) {
+	    $out_file =~ s/\.d$/\.mzML/i;
 	} else {
 	    $command = "$command{echo} Cannot process $file : Unknown type.";
 	    $out_file = "NO_FILE";
-
 	}
+	# did user ask to gzip entire mzml file?
+	$out_file = $out_file.".gz" if (param('msconvert_gzip')); 
 	push @commands, ($command, $out_file);
 
     }
@@ -7473,6 +7476,8 @@
 	'Select instrument file type you want to convert: ',
 	hidden(-name=>'Action',
 	       -value=>$web_actions{'switchRawFile'}),
+	hidden(-name=>'refpage',
+	       -value=>'mzxml'),
 	popup_menu(-name=>'rawfile_type',
 		   -values => [qw'wiff ddir raw rawdir'],
 		   -default => $rawfile,
@@ -7607,13 +7612,44 @@
 ########################################################################
 sub pageMsConvert {
 
-    # files to process (from session)
-    my $any_files_there = &showFiles('mzml','msconvert','raw','1. Specify RAW Input File(s) to convert to mzML');
+    Delete('Action');
 
+    my %labels = ( 'raw'       => 'Thermo RAW',
+		   'rawdir'    => 'Waters .raw Directories',
+		   'wiff'      => 'ABI/Agilent .wiff',
+		   'ddir'      => 'Agilent .d Directories'
+		   );
 
     print
+	&printTitle(title  => '1. Input File Format',
+		    class  => 'formentryhead',
+		    div_id => 'input'),
+	"<div id=input class=formentry>",
+	start_form(-method => 'POST',
+		   -action => $tpp_url,
+		   -name => 'switchRawFile'),
+	'Select instrument file type you want to convert: ',
+	hidden(-name=>'Action',
+	       -value=>$web_actions{'switchRawFile'}),
+	hidden(-name=>'refpage',
+	       -value=>'msconvert'),
+	popup_menu(-name=>'rawfile_type',
+		   -values => [qw'wiff ddir raw rawdir'],
+		   -default => $rawfile,
+		   -labels=>\%labels,
+		   -onChange => 'document.forms.switchRawFile.submit();'),
+	h5('Please note that these converters will only work on machines that contain the appropriate vendor libraries.'),
+	endform,
+	"</div>\n";
+
+    my $choosetype = ($rawfile =~ /dir$/) ? 'DIRS' : $rawfile;
+    my $choosestr  = ($rawfile =~ /dir$/) ? 'Directory(ies)' : 'File(s)';
+    # files to process (from session)
+    my $any_files_there = &showFiles('mzml','msconvert',$choosetype,"2. Specify $choosestr to convert to mzML");
+
+    print
 	br,
-	&printTitle(title  => '2. Conversion Options',
+	&printTitle(title  => '3. Conversion Options',
 		    class  => 'formentryhead',
 		    div_id => 'conv'),
 	"<div id=conv class=formentry>",
@@ -7634,7 +7670,7 @@
 	"Enter additional options to pass directly to the command-line (expert use only!) ",
 	textfield(-name=>'msconvert_extraopts',
 		  -value=>'',
-		  -size=>25,
+		  -size=>50,
 		  -maxlength=>100),
 	"</div>\n";
 


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