--- a/ChipSeqRatioAnalysis.R	Fri Nov 22 07:56:48 2019 -0500
+++ b/ChipSeqRatioAnalysis.R	Mon Dec 02 03:45:28 2019 -0500
@@ -53,7 +53,7 @@
 png(pngfile, width = 1000, height = 1200, pointsize=20)
 par(mfrow=c(2,1))
 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE)
-suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Seq ratio", pch=20, ylim=lims))
+suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Input ratio", pch=20, ylim=lims))
 abline(h=1,col='#00000080', lwd = 2)
 abline(h=2,col='#FF000080', lwd = 2)
 
@@ -82,5 +82,6 @@
        row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top")
 }
 HTMLEndFile(filename) 
-file.rename(from=filename, to=HTMLfile)
+# file.rename(from=filename, to=HTMLfile)
+system(sprintf("cp -r ./%s %s", filename, HTMLfile))
 write.table(df, file=input, sep="\t", row.names = FALSE)

--- a/ChipSeqRatioDef.xml	Fri Nov 22 07:56:48 2019 -0500
+++ b/ChipSeqRatioDef.xml	Mon Dec 02 03:45:28 2019 -0500
@@ -7,6 +7,7 @@
       <requirement type="package">r-base64enc</requirement>
       <requirement type="package">r-r2html</requirement>
       <requirement type="package">blast</requirement>
+      <!-- <requirement type="package">chip_seq_ration</requirement> -->
     </requirements>
     <command interpreter="python3">
 	ChipSeqRatioAnalysis.py 
@@ -26,7 +27,7 @@
 	<param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta"
 	       help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/> 
 	<param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/>   
-	<param name="bitscore" label="Minimum bit score threshold" type="integer" value="30" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/>   
+	<param name="bitscore" label="Minimum bit score threshold" type="integer" value="50" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/>   
     </inputs>
     <outputs>
     	<data name="OutputFile" format="tabular"/>

--- a/paired_fastq_filtering.xml	Fri Nov 22 07:56:48 2019 -0500
+++ b/paired_fastq_filtering.xml	Mon Dec 02 03:45:28 2019 -0500
@@ -1,9 +1,9 @@
-<tool id="paired_fastq_filtering" name="Preprocessing of fastq paired-reads">
+<tool id="paired_fastq_filtering" name="Preprocessing of fastq paired-end reads">
   <stdio>
      <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
   <description>
-    Preprocessing of paired reads fastq files
+    Preprocessing of paired-end reads fastq files
     including trimming, quality filtering, cutadapt filtering and interlacing. Broken
     pairs are discarded.
   </description>
@@ -91,7 +91,7 @@
       </when>
     </conditional>
 
-    <param name="rename" type="boolean" truevalue="-R" falsevalue="" checked="False" label="Rename sequences" help="By default, original sequence ID are used, in case your sequences do not follow proper naming scheme to label paired-end read mate, use this option. All read pairs must be complete!"/>
+    <param name="rename" type="boolean" truevalue="-R" falsevalue="" checked="True" label="Rename sequences" help="By default, original sequence ID are used, in case your sequences do not follow proper naming scheme to label paired-end read mate, use this option. All read pairs must be complete!"/>
   </inputs>