Mercurial > repos > triasteran > ribogalaxy_umi_processing
diff UMI_riboseq_tool/UMI_riboseq.xml @ 10:d003917eaf2c draft
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author | jackcurragh |
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date | Fri, 15 Jul 2022 12:43:45 +0000 |
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children | 3bd2e8301575 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/UMI_riboseq_tool/UMI_riboseq.xml Fri Jul 15 12:43:45 2022 +0000 @@ -0,0 +1,36 @@ +<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.7"> +<requirements> + <requirement type="package" version="1.75">biopython</requirement> +</requirements> +<command detect_errors="exit_code"> +<![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output $gzip $5_prime_UMI_length $3_prime_UMI_length]]> +</command> +<inputs> + <param format="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="5_prime_UMI_length" type="integer" value="2" label="Number of UMI bases at the 5' end" help="2 for McGincy Ingolia Protocol" /> + <param name="3_prime_UMI_length" type="integer" value="5" label="Number of UMI bases at the 3' end)" help="5 for McGincy Ingolia Protocol" /> + +</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> + <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>