<tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8">
<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,fastqsanger.gz" 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 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}, }
</citation>
</citations>
</tool>