# HG changeset patch
# User shian_su <registertonysu@gmail.com>
# Date 1421040708 -39600
# Node ID 5a917ea5bed2f703246c1e3febe55b32eacb1e5d
# Parent  44130e484a976c3ab62fd0377099f4a5e32cbeeb
- Fixed read requirement report statistic.

diff -r 44130e484a97 -r 5a917ea5bed2 hairpinTool.R
--- a/hairpinTool.R	Wed Nov 19 11:05:03 2014 +1100
+++ b/hairpinTool.R	Mon Jan 12 16:31:48 2015 +1100
@@ -417,6 +417,7 @@
                                                   
 if (inputType == "fastq" || inputType == "pairedFastq") {
   # Use EdgeR hairpin process and capture outputs
+
   hpReadout <- capture.output(
   data <- processAmplicons(readfile=fastqPath, readfile2=fastqPathRev,
                             barcodefile=samplePath, 
@@ -988,7 +989,7 @@
 }
 
 if (sampleReq != 0) {
-  tempStr <- paste("Samples that did not produce more than", sampleReq,
+  tempStr <- paste("Samples that did not produce more than", readReq,
                    "counts were filtered out.")
   ListItem(tempStr)
 
diff -r 44130e484a97 -r 5a917ea5bed2 hairpinTool.xml
--- a/hairpinTool.xml	Wed Nov 19 11:05:03 2014 +1100
+++ b/hairpinTool.xml	Mon Jan 12 16:31:48 2015 +1100
@@ -81,7 +81,7 @@
                 #end if
                 
                 #if $inputOpt.secondaryFactor.secFactorOpt=="yes":
-                  $inputOpt.secondaryFactor.secFactName
+                  "$inputOpt.secondaryFactor.secFactName"
                 #else:
                   "none"
                 #end if
@@ -96,23 +96,23 @@
                   -Inf
                 #end if
           
-                $fdr
-                $lfc
-                $direction
-                $workMode.mode
-                $outFile
-                $outFile.files_path
+                "$fdr"
+                "$lfc"
+                "$direction"
+                "$workMode.mode"
+                "$outFile"
+                "$outFile.files_path"
           
                 #if $workMode.mode=="classic":
                   "$workMode.pair1"
                   "$workMode.pair2"
                 #elif $workMode.mode=="glm":
                   "$workMode.contrast"
-                  $workMode.roast.roastOption
+                  "$workMode.roast.roastOption"
 
                   #if $workMode.roast.roastOption=="yes":
-                    $workMode.roast.hairpinReq
-                    $workMode.roast.select.selOption
+                    "$workMode.roast.hairpinReq"
+                    "$workMode.roast.select.selOption"
                     "$workMode.roast.select.selection"
                   #else:
                     0