Mercurial > repos > triasteran > ribogalaxy_umi_processing
diff UMI_riboseq_processing/UMI_riboseq.xml @ 4:a580e700aac3 draft
Uploaded
author | triasteran |
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date | Tue, 21 Jun 2022 08:32:44 +0000 |
parents | d27375bc4a1c |
children | e370df93715d |
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--- a/UMI_riboseq_processing/UMI_riboseq.xml Mon Jun 20 08:02:35 2022 +0000 +++ b/UMI_riboseq_processing/UMI_riboseq.xml Tue Jun 21 08:32:44 2022 +0000 @@ -1,5 +1,6 @@ -<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.3"> +<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.4"> <requirements> + <requirement type="package" version="1.75">biopython</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]> @@ -17,7 +18,8 @@ </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]]> +<![CDATA[ fastq/fastq.gz are input files with reads containing UMIs (already demultiplexed and adapters are removed). + 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. It is designed for protocol: McGlincy NJ, Ingolia NT. Transcriptome-wide measurement of translation by ribosome profiling. Methods. 2017;126:112-129. doi:10.1016/j.ymeth.2017.05.028 ]]> </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}, }