Mercurial > repos > triasteran > ribogalaxy_umi_processing
view UMI_riboseq_tool/UMI_riboseq.xml @ 19:30e979789d8f draft default tip
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author | triasteran |
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date | Fri, 30 Sep 2022 11:02:28 +0000 |
parents | 106ef893af60 |
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<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.12"> <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}]]> </command> <inputs> <param format="fastq,fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" /> <param name="five_prime_UMI_length" type="integer" value='2' label="Number of UMI bases at the 5' end" help="2 for McGlincy Ingolia Protocol" /> <param name="three_prime_UMI_length" type="integer" value='5' label="Number of UMI bases at the 3' end)" help="5 for McGlincy Ingolia Protocol" /> </inputs> <outputs> <data format="fastq.gz" name="output"/> </outputs> <tests> <test> <param name="reads" value="sub_10k_reads.fq.gz"/> <output name="output" file="output"/> </test> <test> <param name="reads" value="sub_10k_reads2.fq"/> <output name="output" file="output2"/> </test> </tests> <help> <![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}, } </citation> </citations> </tool>