comparison UMI_riboseq_processing/UMI_riboseq.xml @ 4:a580e700aac3 draft

Uploaded

3:d27375bc4a1c

<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.3">
<requirements>
</requirements>
<command detect_errors="exit_code">
<![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]>
</command>
<inputs>

        <param name="reads" value="sub_10k_reads.fq.gz"/>
        <output name="output" file="output"/>
    </test>
</tests>
<help>
<![CDATA[ **fastq/fastq.gz** input files with reads containing both UMIs and barcodes but NO adapters. ----- **Output** 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; next step of processing is demultiplexing]]>
</help>
<citations>
<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}, }
</citation>
</citations>

4:a580e700aac3

<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.4">
<requirements>
  <requirement type="package" version="1.75">biopython</requirement>
</requirements>
<command detect_errors="exit_code">
<![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]>
</command>
<inputs>

        <param name="reads" value="sub_10k_reads.fq.gz"/>
        <output name="output" file="output"/>
    </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, 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}, }
</citation>
</citations>