Mercurial > repos > jackcurragh > ribogalaxy_umi_extraction
comparison UMI_riboseq_tool/UMI_riboseq.xml @ 1:4605a1af1f3d draft default tip
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author | triasteran |
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date | Fri, 30 Sep 2022 09:07:04 +0000 |
parents | 393b73b2eb5f |
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0:393b73b2eb5f | 1:4605a1af1f3d |
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1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8"> | 1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="1.75">biopython</requirement> | 3 <requirement type="package" version="1.75">biopython</requirement> |
4 </requirements> | 4 </requirements> |
5 <command detect_errors="exit_code"> | 5 <command detect_errors="exit_code"> |
6 <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output $gzip $five_prime_UMI_length $three_prime_UMI_length]]> | 6 <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output $gzip $5_prime_UMI_length $3_prime_UMI_length]]> |
7 </command> | 7 </command> |
8 <inputs> | 8 <inputs> |
9 <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> | 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" /> | 10 <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" /> |
11 <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" /> | 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="three_prime_UMI_length" type="integer" value=5 label="Number of UMI bases at the 3' end)" help="5 for McGlincy 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 | 13 |
14 </inputs> | 14 </inputs> |
15 <outputs> | 15 <outputs> |
16 <data format="fastqsanger" name="output"/> | 16 <data format="fastqsanger,fastqsanger.gz" name="output"/> |
17 </outputs> | 17 </outputs> |
18 <tests> | 18 <tests> |
19 <test> | 19 <test> |
20 <param name="reads" value="sub_10k_reads.fq.gz"/> | 20 <param name="reads" value="sub_10k_reads.fq.gz"/> |
21 <output name="output" file="output"/> | 21 <output name="output" file="output"/> |
28 <help> | 28 <help> |
29 <![CDATA[ fastq/fastq.gz are input files with reads containing UMIs (already demultiplexed and adapters are removed). | 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 ]]> | 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> | 31 </help> |
32 <citations> | 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}, } | 33 <citation type="bibtex"> @misc{FedorovaAD2022 and TierneyJack2022, author = {Fedorova Alla, Tierney Jack}, 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> | 34 </citation> |
35 </citations> | 35 </citations> |
36 </tool> | 36 </tool> |