Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 32:7c33029fd63d draft

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Uploaded
author davidvanzessen
date Tue, 28 Mar 2017 05:40:04 -0400
parents b539aeb75980
children 6603110e5be3
comparison
equal deleted inserted replaced
31:3a76faa53c59 32:7c33029fd63d
116 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile 116 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
117 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile 117 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
118 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile 118 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
119 119
120 120
121 echo "<img src='VFPlot.png'/>" >> $outputFile 121 echo "<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>" >> $outputFile
122 if [[ "$useD" == "true" ]] ; then 122 if [[ "$useD" == "true" ]] ; then
123 echo "<img src='DFPlot.png'/>" >> $outputFile 123 echo "<a href='DFPlot.pdf'><img src='DFPlot.png'/></a>" >> $outputFile
124 fi 124 fi
125 echo "<img src='VPlot.png'/>" >> $outputFile 125 echo "<a href='VPlot.pdf'><img src='VPlot.png'/></a>" >> $outputFile
126 if [[ "$useD" == "true" ]] ; then 126 if [[ "$useD" == "true" ]] ; then
127 echo "<img src='DPlot.png'/>" >> $outputFile 127 echo "<a href='DPlot.pdf'><img src='DPlot.png'/></a>" >> $outputFile
128 fi 128 fi
129 echo "<img src='JPlot.png'/> <br />" >> $outputFile 129 echo "<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />" >> $outputFile
130 130
131 echo "<img src='DReadingFrame.png'/>" >> $outputFile 131 echo "<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>" >> $outputFile
132 132
133 cat $dir/naive_gene_freq.htm >> $outputFile 133 cat $dir/naive_gene_freq.htm >> $outputFile
134 134
135 echo "</div>" >> $outputFile 135 echo "</div>" >> $outputFile
136 136
137 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile 137 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
138 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile 138 echo "<a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br />" >> $outputFile
139 echo "<img src='AAComposition.png'/>" >> $outputFile 139 echo "<a href='AAComposition.pdf'><img src='AAComposition.png'/></a>" >> $outputFile
140 140
141 141
142 echo "<table class='pure-table pure-table-striped'>" >> $outputFile 142 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
143 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile 143 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
144 while read Sample median 144 while read Sample median
156 count=1 156 count=1
157 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile 157 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
158 for sample in $samples; do 158 for sample in $samples; do
159 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile 159 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
160 if [[ "$useD" == "true" ]] ; then 160 if [[ "$useD" == "true" ]] ; then
161 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile 161 echo "<td><a href='HeatmapVD_$sample.pdf'><img src='HeatmapVD_$sample.png'/></a></td>" >> $outputFile
162 fi 162 fi
163 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile 163 echo "<td><a href='HeatmapVJ_$sample.pdf'><img src='HeatmapVJ_$sample.png'/></a></td>" >> $outputFile
164 if [[ "$useD" == "true" ]] ; then 164 if [[ "$useD" == "true" ]] ; then
165 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile 165 echo "<td><a href='HeatmapDJ_$sample.pdf'><img src='HeatmapDJ_$sample.png'/></a></td>" >> $outputFile
166 fi 166 fi
167 echo "</tr></table></div>" >> $outputFile 167 echo "</tr></table></div>" >> $outputFile
168 count=$((count+1)) 168 count=$((count+1))
169 done 169 done
170 170
192 192
193 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile 193 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
194 for sample in $samples; do 194 for sample in $samples; do
195 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile 195 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
196 if [[ "$useD" == "true" ]] ; then 196 if [[ "$useD" == "true" ]] ; then
197 echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile 197 echo "<tr><td>V-D</td><td><a href='circosVD_${sample}.pdf'><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
198 fi 198 fi
199 echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile 199 echo "<tr><td>V-J</td><td><a href='circosVJ_${sample}.pdf'><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
200 if [[ "$useD" == "true" ]] ; then 200 if [[ "$useD" == "true" ]] ; then
201 echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile 201 echo "<tr><td>D-J</td><td><a href='circosDJ_${sample}.pdf'><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
202 fi 202 fi
203 echo "<center></table></div>" >> $outputFile 203 echo "<center></table></div>" >> $outputFile
204 count=$((count+1)) 204 count=$((count+1))
205 done 205 done
206 206