Mercurial > repos > davidvanzessen > vidjil_with_browser
changeset 7:e55dfd9a8c00 draft default tip
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 12 Feb 2015 10:47:15 -0500 |
| parents | 7346cd210a43 |
| children | |
| files | vidjil.sh vidjil.xml |
| diffstat | 2 files changed, 21 insertions(+), 45 deletions(-) [+] |
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--- 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 "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $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 "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $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; +
--- 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 @@ <tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0"> <description></description> <command interpreter="bash"> - 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 </command> <inputs> - <repeat name="in_files" title="Input Files" min="1" default="1"> - <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" /> - <param name="id" type="text" label="ID" /> - </repeat> + <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" /> + <param name="id" type="text" label="ID" /> <param name="database" type="select" label="Database"> <option value="current">Germline database from IMGT of 30-9-14</option> <option value="download">Download newest database from IMGT</option> @@ -34,7 +28,8 @@ <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/> </inputs> <outputs> - <data format="html" name="out_file" label="Vidjil on blah"/> + <data format="html" name="out_file" label="Vidjil browser of ${in_file.name}"/> + <data format="fasta" name="fasta_out" label="Vidjil fasta of ${in_file.name}" /> </outputs> <help> A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.