Mercurial > repos > stef > qdnaseq
changeset 67:2d939f4c23fe draft
Uploaded
| author | stef |
|---|---|
| date | Tue, 26 Aug 2014 07:38:40 -0400 |
| parents | 823791a3d7e1 |
| children | 68a090cffb6f |
| files | LGG150_calls_example.png LGG150_copynumber_example.png QDNAseq.R QDNAseq.css QDNAseq.xml static/css/QDNAseq.css static/images/LGG150_copynumber_example.png |
| diffstat | 7 files changed, 12 insertions(+), 13 deletions(-) [+] |
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--- a/QDNAseq.R Wed Aug 20 11:22:43 2014 -0400 +++ b/QDNAseq.R Tue Aug 26 07:38:40 2014 -0400 @@ -135,7 +135,7 @@ ## ================================================== MAIN_NAME <- '[INFO] ' TOOL_PATH <- getScriptPath() -CSS_FILE <- paste( TOOL_PATH, '/QDNAseq.css', sep="" ) +CSS_FILE <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" ) DECIMALS <- 3 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html' PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css' @@ -299,7 +299,7 @@ png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); par( PAR_SET ) plot( copyNumbersSmooth[ ,sample ], main=paste(sample, ": CopyNumbers", sep="") ); - mtext( paste( "(", binSizeString, " bins)", sep=""), 3 ) + mtext( paste( "(", binSizeString, " bins)" sep=""), 3 ) abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) dev.off() @@ -314,7 +314,7 @@ png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); par( PAR_SET ) plot( copyNumbersSegmented[ ,sample ], main=paste(sample, ": CopyNumbers and Segments", sep="") ); - mtext( paste( "(", binSizeString, " bins)", sep=""), 3 ) + mtext( paste( "(", binSizeString, " bins)" sep=""), 3 ) abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) dev.off()
--- a/QDNAseq.css Wed Aug 20 11:22:43 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -/* --- QDNAseq CSS --- */ -body{ padding: 0px 20px; } -pre { padding: 0px 25px; } -h3.qdnaseq{ color: #355681; border-bottom: 1px solid #355681;} -.marker { background: yellow; color: red;} -.button { background: rgb(28, 184, 65); color: white; border-radius: 4px; padding: 4px 10px }
--- a/QDNAseq.xml Wed Aug 20 11:22:43 2014 -0400 +++ b/QDNAseq.xml Tue Aug 26 07:38:40 2014 -0400 @@ -6,14 +6,13 @@ <!-- <requirement type="package" version="3.1.0">R</requirement> --> <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> --> <requirement type="package" version="0.1.18">samtools</requirement> - <requirement type="set_environment">TOOL_DIR</requirement> </requirements> <description>Quantitative copy number abberation detection</description> <!-- command block to call script with default R installation --> <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) --> - <command interpreter="Rscript"> + <command interpreter="/ccagc/lib/R/R-3.1.0/bin/Rscript"> QDNAseq.R $qdnaseq_cfg </command> @@ -55,7 +54,7 @@ <!-- ==================== --> <!-- Input BAMs --> <!-- ==================== --> - <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select the BAM files to analyze" /> + <param name="bams" type="data" multiple="true" optional="True" format="bam" label="Input BAMs" help="Select the BAM files to analyze" /> <!-- ==================== --> <!-- Optional segmenting --> @@ -284,7 +283,7 @@ .. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html -.. image:: ./LGG150_copynumber_example.png :height: 240 :width: 480 +.. image:: LGG150_copynumber_example.png :height: 240 :width: 480 </help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/css/QDNAseq.css Tue Aug 26 07:38:40 2014 -0400 @@ -0,0 +1,6 @@ +/* --- QDNAseq CSS --- */ +body{ padding: 0px 20px; } +pre { padding: 0px 25px; } +h3.qdnaseq{ color: #355681; border-bottom: 1px solid #355681;} +.marker { background: yellow; color: red;} +.button { background: rgb(28, 184, 65); color: white; border-radius: 4px; padding: 4px 10px }