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1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8">
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2 <requirements>
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3 <requirement type="package" version="1.75">biopython</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code">
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6 <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output $gzip $five_prime_UMI_length $three_prime_UMI_length]]>
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7 </command>
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8 <inputs>
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9 <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/>
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10 <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" />
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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" />
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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" />
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13
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14 </inputs>
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15 <outputs>
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16 <data format="fastqsanger" name="output"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="reads" value="sub_10k_reads.fq.gz"/>
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21 <output name="output" file="output"/>
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22 </test>
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23 <test>
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24 <param name="reads" value="sub_10k_reads2.fq"/>
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25 <output name="output" file="output2"/>
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26 </test>
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27 </tests>
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28 <help>
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29 <![CDATA[ fastq/fastq.gz are input files with reads containing UMIs (already demultiplexed and adapters are removed).
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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 ]]>
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31 </help>
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32 <citations>
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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}, }
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34 </citation>
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35 </citations>
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36 </tool>
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