| Previous changeset 5:378565f5a875 (2019-11-22) Next changeset 7:89c5ba120b21 (2019-12-02) |
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modified:
ChipSeqRatioAnalysis.R ChipSeqRatioDef.xml paired_fastq_filtering.xml |
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| diff -r 378565f5a875 -r f224513123a1 ChipSeqRatioAnalysis.R --- a/ChipSeqRatioAnalysis.R Fri Nov 22 07:56:48 2019 -0500 +++ b/ChipSeqRatioAnalysis.R Mon Dec 02 03:45:28 2019 -0500 |
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| @@ -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) |
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| diff -r 378565f5a875 -r f224513123a1 ChipSeqRatioDef.xml --- a/ChipSeqRatioDef.xml Fri Nov 22 07:56:48 2019 -0500 +++ b/ChipSeqRatioDef.xml Mon Dec 02 03:45:28 2019 -0500 |
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| @@ -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"/> |
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| diff -r 378565f5a875 -r f224513123a1 paired_fastq_filtering.xml --- 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 |
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| @@ -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> |