Mercurial > repos > triasteran > ribogalaxy_umi_processing
changeset 16:cf1a0cbe5c34 draft
Uploaded
| author | triasteran |
|---|---|
| date | Fri, 30 Sep 2022 09:27:53 +0000 |
| parents | b90ecf790d5b |
| children | 42f195d0ed6d |
| files | UMI_riboseq_tool/UMI.py UMI_riboseq_tool/UMI_riboseq.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/UMI_riboseq_tool/UMI.py Mon Jul 25 12:40:07 2022 +0000 +++ b/UMI_riboseq_tool/UMI.py Fri Sep 30 09:27:53 2022 +0000 @@ -50,7 +50,7 @@ print ('file is gzipped fastq') with gzip.open(pathToFastaFile, "rt") as handle: for i, record in enumerate(SeqIO.parse(handle, "fastq")): - process_fastq_record(record, output, UMI_5_prime_length=2, UMI_3_prime_length=5) + process_fastq_record(record, output, UMI_5_prime_length, UMI_3_prime_length) else: for record in SeqIO.parse(pathToFastaFile, 'fastq'):
--- a/UMI_riboseq_tool/UMI_riboseq.xml Mon Jul 25 12:40:07 2022 +0000 +++ b/UMI_riboseq_tool/UMI_riboseq.xml Fri Sep 30 09:27:53 2022 +0000 @@ -1,9 +1,9 @@ -<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8"> +<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.9"> <requirements> <requirement type="package" version="1.75">biopython</requirement> </requirements> <command detect_errors="exit_code"> -<![CDATA[ python3 $__tool_directory__/UMI.py $reads $output $gzip $five_prime_UMI_length $three_prime_UMI_length]]> +<![CDATA[ python3 $__tool_directory__/UMI.py $reads $output $gzip ${five_prime_UMI_length} ${three_prime_UMI_length}]]> </command> <inputs> <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> @@ -13,7 +13,7 @@ </inputs> <outputs> - <data format="fastqsanger" name="output"/> + <data format="fastqsanger,fastqsanger.gz" name="output"/> </outputs> <tests> <test>