comparison report_clonality/r_wrapper.sh @ 57:33412e85e669 draft

"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"

56:7ae6b6b5d890

clonalType=$4
species=$5
locus=$6
filterproductive=$7
clonality_method=$8

dir="$(cd "$(dirname "$0")" && pwd)"
useD="false"
if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
	echo "species D region in reference db"

	cat $dir/naive_junction.htm >> $outputFile
	
	echo "</div>" >> $outputFile
fi

echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
echo "<table class='pure-table pure-table-striped'>" >> $outputFile
echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile

echo "<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>" >> $outputFile
if [[ "$useD" == "true" ]] ; then

57:33412e85e669

clonalType=$4
species=$5
locus=$6
filterproductive=$7
clonality_method=$8

ALL_OUTPUTS_ZIP="$outputDir/all_outputs.zip"

dir="$(cd "$(dirname "$0")" && pwd)"
useD="false"
if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
	echo "species D region in reference db"

	cat $dir/naive_junction.htm >> $outputFile
	
	echo "</div>" >> $outputFile
fi


# Create zip file with all download files
# Use 7za as it is packaged in the container already.
cd "$outputDir" || exit 1

7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
  allUnique.txt VFFrequency.txt VFrequency.txt \
  JFrequency.txt DReadingFrame.txt CDR3LengthPlot.txt \
  AAComposition.txt clonalityComplete.txt

if [[ "$useD" == "true" ]] ; then
  7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
  DFFrequency.txt DFrequency.txt
fi
for sample in $samples; do
  if [[ "$useD" == "true" ]] ; then
    7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
    "HeatmapVD_$sample.txt" "HeatmapDJ_$sample.txt" \
    "${sample}_VD_circos.txt" "${sample}_DJ_circos.txt"
  fi
  7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
  "HeatmapVJ_$sample.txt" "${sample}_VJ_circos.txt"
done

cd $dir || exit 1

echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
echo "<table class='pure-table pure-table-striped'>" >> $outputFile
echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
echo "<tr><td>All outputs below in a zip file</td><td><a href='$ALL_OUTPUTS_ZIP'>Download</a></td></tr>" >> $outputFile
echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile

echo "<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>" >> $outputFile
if [[ "$useD" == "true" ]] ; then