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1 <tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.4">
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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 ]]>
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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 </inputs>
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11 <outputs>
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12 <data format="fastqsanger" name="output"/>
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13 </outputs>
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14 <tests>
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15 <test>
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16 <param name="reads" value="sub_10k_reads.fq.gz"/>
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17 <output name="output" file="output"/>
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18 </test>
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19 </tests>
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20 <help>
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21 <![CDATA[ fastq/fastq.gz are input files with reads containing UMIs (already demultiplexed and adapters are removed).
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22 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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23 </help>
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24 <citations>
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25 <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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26 </citation>
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27 </citations>
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2
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28 </tool>
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