Mercurial > repos > triasteran > ribogalaxy_umi_processing
comparison UMI_riboseq_tool/UMI_riboseq.xml @ 17:42f195d0ed6d draft
Uploaded
| author | triasteran |
|---|---|
| date | Fri, 30 Sep 2022 09:44:28 +0000 |
| parents | cf1a0cbe5c34 |
| children | 106ef893af60 |
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| 16:cf1a0cbe5c34 | 17:42f195d0ed6d |
|---|---|
| 1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.9"> | 1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.10"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="1.75">biopython</requirement> | 3 <requirement type="package" version="1.75">biopython</requirement> |
| 4 </requirements> | 4 </requirements> |
| 5 <command detect_errors="exit_code"> | 5 <command detect_errors="exit_code"> |
| 6 <![CDATA[ python3 $__tool_directory__/UMI.py $reads $output $gzip ${five_prime_UMI_length} ${three_prime_UMI_length}]]> | 6 <![CDATA[ python3 $__tool_directory__/UMI.py $reads $output $gzip ${five_prime_UMI_length} ${three_prime_UMI_length}]]> |
| 7 </command> | 7 </command> |
| 8 <inputs> | 8 <inputs> |
| 9 <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> | 9 <param format="fastq,fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> |
| 10 <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" /> | 10 <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" /> |
| 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" /> | 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" /> |
| 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" /> | 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" /> |
| 13 | 13 |
| 14 </inputs> | 14 </inputs> |
| 15 <outputs> | 15 <outputs> |
| 16 <data format="fastqsanger,fastqsanger.gz" name="output"/> | 16 <data format="fastq,fastqsanger,fastqsanger.gz" name="output"/> |
| 17 </outputs> | 17 </outputs> |
| 18 <tests> | 18 <tests> |
| 19 <test> | 19 <test> |
| 20 <param name="reads" value="sub_10k_reads.fq.gz"/> | 20 <param name="reads" value="sub_10k_reads.fq.gz"/> |
| 21 <output name="output" file="output"/> | 21 <output name="output" file="output"/> |