# HG changeset patch
# User davidvanzessen
# Date 1423756035 18000
# Node ID e55dfd9a8c0089072ab1b3fa21c5cc25c242f723
# Parent 7346cd210a4308fb7e99c0503c2b39667e73a838
Uploaded
diff -r 7346cd210a43 -r e55dfd9a8c00 vidjil.sh
--- a/vidjil.sh Thu Feb 12 09:54:07 2015 -0500
+++ b/vidjil.sh Thu Feb 12 10:47:15 2015 -0500
@@ -2,21 +2,24 @@
set -e
inputFile=$1
-outputFile=$2
-outputDir=$3
-database=$4
-limit_reads=$5
-limit_ratio=$6
-selection=$7
-germline=$8
+id=$2
+outputFile=$3
+outputDir=$4
+database=$5
+limit_reads=$6
+limit_ratio=$7
+selection=$8
+germline=$9
+fastaFile=${10}
+wd="$PWD"
dir="$(cd "$(dirname "$0")" && pwd)"
mkdir $outputDir
+mkdir $outputDir/data
+echo "Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $outputFile
unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log
-mkdir $outputDir/data
-
if [[ "$database" == "download" ]] ; then
echo "Downloading up to date database from IMGT..."
mkdir $outputDir/tmp
@@ -31,34 +34,12 @@
cd $dir
fi
+./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $inputFile
-inputFiles=$(echo "$inputFile" | tr "| " "\n")
-files_for_config=""
-last_file=""
-for id_file in $inputFiles
-do
- tmp=($(echo "${id_file}" | tr ";" "\n"))
- id=${tmp[0]}
- file=${tmp[1]}
-
- ./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $file
-
- if [[ "$files_for_config" != "" ]] ; then
- files_for_config="${files_for_config},"
- fi
- files_for_config="${files_for_config}'${id}.vidjil'"
- last_file="${id}.vidjil"
-done
-
-echo "Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $outputFile
+mv $outputDir/data/${id}.vdj.fa $fastaFile
echo -e \
"var config = {\n" \
-" 'file_menu' : {\n" \
-" 'path' : 'data/',\n" \
-" 'file' : [\n" \
-" ${files_for_config}\n" \
-" ]\n" \
-" },\n" \
-" 'autoload' : 'data/${last_file}'\n" \
+" 'autoload' : 'data/${id}.vidjil'\n" \
"}" > $outputDir/js/conf.js;
+
diff -r 7346cd210a43 -r e55dfd9a8c00 vidjil.xml
--- a/vidjil.xml Thu Feb 12 09:54:07 2015 -0500
+++ b/vidjil.xml Thu Feb 12 10:47:15 2015 -0500
@@ -1,17 +1,11 @@
- vidjil.sh "
-#for $i, $f in enumerate($in_files)
-${f.id};${f.in_file}|
-#end for
-" $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline
+ vidjil.sh $in_file $id $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline $fasta_out
-
-
-
-
+
+
@@ -34,7 +28,8 @@
-
+
+
A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.