Mercurial > repos > davidvanzessen > imgt_convert
changeset 6:a43100e5d032 draft
Deleted selected files
| author | davidvanzessen |
|---|---|
| date | Tue, 10 Dec 2013 07:55:34 -0500 |
| parents | 0544b052af07 |
| children | a7fe6f068f83 |
| files | plotting_merged.xml r_wrapper.sh |
| diffstat | 2 files changed, 0 insertions(+), 50 deletions(-) [+] |
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--- a/plotting_merged.xml Tue Dec 10 07:26:10 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -<tool id="test_plotting_merged" name="TEST-Plotting the merged data-TEST" version="1.0"> - <description>Creating a graph of the merged reports.</description> - <command interpreter="bash"> - r_wrapper.sh $in_file $out_file $out_file.files_path - </command> - <inputs> - <param name="in_file" format="tabular" type="data" label="Data to Process" /> - </inputs> - <outputs> - <data format="html" name="out_file" /> - </outputs> - <help> - Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J) - </help> -</tool>
--- a/r_wrapper.sh Tue Dec 10 07:26:10 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -#!/bin/bash -echo $1 -echo $2 -echo $3 - -inputFile=$1 -outputFile=$2 -outputDir=$3 -dir="$(cd "$(dirname "$0")" && pwd)" -mkdir $3 -Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1 -echo "<html>" >> $2 -echo "<img src='VPlot.png'/>" >> $2 -echo "<img src='DPlot.png'/>" >> $2 -echo "<img src='JPlot.png'/>" >> $2 - -samples=`cat $outputDir/samples.txt` -count=1 -echo "<table border='1'>" >> $outputFile -for sample in $samples; do - echo "<tr><td colspan='3' height='100'></td>" >> $outputFile - echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile - echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile - mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" - echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile - mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" - echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile - mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" - echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile - count=$((count+1)) -done -echo "</table>" >> $outputFile - -echo "</html>" >> $2 -