comparison UMI_riboseq_processing/UMI_riboseq.xml @ 8:701804f5ad4b draft

Uploaded

7:be394fb47250

<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.6a">
<requirements>
</requirements>
<command detect_errors="exit_code">
<![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]>
</command>

<tests>
    <test>
        <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>

8:701804f5ad4b

<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.6c">
<requirements>
</requirements>
<command detect_errors="exit_code">
<![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]>
</command>

<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>