Mercurial > repos > triasteran > ribogalaxy_umi_processing
comparison 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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9:31438c26afec | 10:d003917eaf2c |
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1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.7"> | |
2 <requirements> | |
3 <requirement type="package" version="1.75">biopython</requirement> | |
4 </requirements> | |
5 <command detect_errors="exit_code"> | |
6 <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output $gzip $5_prime_UMI_length $3_prime_UMI_length]]> | |
7 </command> | |
8 <inputs> | |
9 <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> | |
10 <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" /> | |
11 <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" /> | |
12 <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" /> | |
13 | |
14 </inputs> | |
15 <outputs> | |
16 <data format="fastqsanger" name="output"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="reads" value="sub_10k_reads.fq.gz"/> | |
21 <output name="output" file="output"/> | |
22 </test> | |
23 <test> | |
24 <param name="reads" value="sub_10k_reads2.fq"/> | |
25 <output name="output" file="output2"/> | |
26 </test> | |
27 </tests> | |
28 <help> | |
29 <![CDATA[ fastq/fastq.gz are input files with reads containing UMIs (already demultiplexed and adapters are removed). | |
30 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 ]]> | |
31 </help> | |
32 <citations> | |
33 <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}, } | |
34 </citation> | |
35 </citations> | |
36 </tool> |