Mercurial > repos > triasteran > ribogalaxy_umi_processing
view UMI_riboseq_processing/UMI_riboseq.xml @ 2:6958515efa76 draft
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author | triasteran |
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date | Mon, 20 Jun 2022 07:27:23 +0000 |
parents | 5d0d5933d370 |
children | d27375bc4a1c |
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<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.2"> <requirements> </requirements> <command detect_errors="exit_code"> <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]> </command> <inputs> <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> </inputs> <outputs> <data format="fastqsanger" name="output"/> </outputs> <tests> <test> <param name="reads" value="sub_10k_reads.fq.gz"/> <output name="output" file="output"/> </test> </tests> <help> <![CDATA[ **fastq/fastq.gz** input files with reads containing both UMIs and barcodes but NO adapters. ----- **Output** The output of the script is fastq/fastq.gz file where UMIs (7nt in total, 5'NN and 3'NNNNN preceding barcode consisting of 5nt) are in header of the read; next step of processing is demultiplexing]]> </help> <citations> <citation type="bibtex"> @misc{FedorovaAD2022, author = {Fedorova Alla}, year = {2022}, title = {UMI_for_riboseq}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/triasteran/RiboGalaxy_with_ansible/blob/main/toolshed_tools/UMI_riboseq_tool/UMI.py}, } </citation> </citations> </tool>