Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/r_wrapper.sh @ 32:7c33029fd63d draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 28 Mar 2017 05:40:04 -0400 |
| parents | b539aeb75980 |
| children | 6603110e5be3 |
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--- a/report_clonality/r_wrapper.sh Tue Mar 14 06:51:38 2017 -0400 +++ b/report_clonality/r_wrapper.sh Tue Mar 28 05:40:04 2017 -0400 @@ -118,25 +118,25 @@ echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile -echo "<img src='VFPlot.png'/>" >> $outputFile +echo "<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "<img src='DFPlot.png'/>" >> $outputFile + echo "<a href='DFPlot.pdf'><img src='DFPlot.png'/></a>" >> $outputFile fi -echo "<img src='VPlot.png'/>" >> $outputFile +echo "<a href='VPlot.pdf'><img src='VPlot.png'/></a>" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "<img src='DPlot.png'/>" >> $outputFile + echo "<a href='DPlot.pdf'><img src='DPlot.png'/></a>" >> $outputFile fi -echo "<img src='JPlot.png'/> <br />" >> $outputFile +echo "<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />" >> $outputFile -echo "<img src='DReadingFrame.png'/>" >> $outputFile +echo "<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>" >> $outputFile cat $dir/naive_gene_freq.htm >> $outputFile echo "</div>" >> $outputFile echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile -echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile -echo "<img src='AAComposition.png'/>" >> $outputFile +echo "<a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br />" >> $outputFile +echo "<a href='AAComposition.pdf'><img src='AAComposition.png'/></a>" >> $outputFile echo "<table class='pure-table pure-table-striped'>" >> $outputFile @@ -158,11 +158,11 @@ for sample in $samples; do echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile + echo "<td><a href='HeatmapVD_$sample.pdf'><img src='HeatmapVD_$sample.png'/></a></td>" >> $outputFile fi - echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile + echo "<td><a href='HeatmapVJ_$sample.pdf'><img src='HeatmapVJ_$sample.png'/></a></td>" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile + echo "<td><a href='HeatmapDJ_$sample.pdf'><img src='HeatmapDJ_$sample.png'/></a></td>" >> $outputFile fi echo "</tr></table></div>" >> $outputFile count=$((count+1)) @@ -194,11 +194,11 @@ for sample in $samples; do echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + echo "<tr><td>V-D</td><td><a href='circosVD_${sample}.pdf'><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile fi - echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + echo "<tr><td>V-J</td><td><a href='circosVJ_${sample}.pdf'><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + echo "<tr><td>D-J</td><td><a href='circosDJ_${sample}.pdf'><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile fi echo "<center></table></div>" >> $outputFile count=$((count+1))