Mercurial > repos > shians > shrnaseq
changeset 15:5a917ea5bed2
- Fixed read requirement report statistic.
| author | shian_su <registertonysu@gmail.com> |
|---|---|
| date | Mon, 12 Jan 2015 16:31:48 +1100 |
| parents | 44130e484a97 |
| children | 525bf4364896 |
| files | hairpinTool.R hairpinTool.xml |
| diffstat | 2 files changed, 12 insertions(+), 11 deletions(-) [+] |
line wrap: on
line diff
--- 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)
--- 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