Mercurial > repos > davidvanzessen > sff_extract_demultiplex
changeset 10:5a886d753c0a draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 25 Nov 2015 05:02:54 -0500 |
| parents | 7973dd7a39ab |
| children | b59783f3d3ba |
| files | demultiplex.xml wrapper.sh |
| diffstat | 2 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/demultiplex.xml Tue Nov 04 09:16:17 2014 -0500 +++ b/demultiplex.xml Wed Nov 25 05:02:54 2015 -0500 @@ -4,7 +4,7 @@ <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> <command interpreter="bash"> - wrapper.sh $input $out_file $out_file.files_path $where $mismatches $partial $input.name + wrapper.sh "$input" "$out_file" "$out_file.files_path" "$where" "$mismatches" "$partial" "$input.name" #for $i, $b in enumerate($barcodes) "$b.id" "$b.mid" @@ -340,7 +340,7 @@ <data format="html" name="out_file" /> </outputs> <help> -- Splitting sff files into FASTQ, FASTA and (optional) trimmed FASTA files with a FASTQC report on the FASTQ file, this tool uses: +- Splitting sff or fastq files into FASTQ, FASTA and (optional) trimmed FASTA files with a FASTQC report on the FASTQ file, this tool uses: - sff2fastq (https://github.com/indraniel/sff2fastq) to extract a fastq file. - fastx_barcode_splitter.pl (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html) to demultiplex. - fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to provide analysis of the fastq files.
--- a/wrapper.sh Tue Nov 04 09:16:17 2014 -0500 +++ b/wrapper.sh Wed Nov 25 05:02:54 2015 -0500 @@ -1,11 +1,11 @@ #!/bin/bash -input=$1 -output=$2 -outDir=$3 -mkdir $outDir -EOL=$4 -mismatches=$5 -partial=$6 +input="$1" +output="$2" +outDir="$3" +mkdir "$outDir" +EOL="$4" +mismatches="$5" +partial="$6" name=$(basename "$7") ext="${name##*.}" name="${name%.*}" @@ -23,7 +23,7 @@ start_int=$((i+2)) end_int=$((i+3)) id="${!i}" - echo "$id" + echo "$id, ${start_int}, ${end_int}" trim_start[$id]=${!start_int} trim_end[$id]=${!end_int} echo -e "$id\t${!j}" >> $outDir/barcodes.txt