Mercurial > repos > kkonganti > centrifuge_process
comparison centrifuge_process.xml @ 0:00fa638e833e
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 22 Jun 2022 16:13:46 -0400 |
| parents | |
| children | 48eebe68ec69 |
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| -1:000000000000 | 0:00fa638e833e |
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| 1 <tool id="centrifuge_process" name="Take in centrifuge output, report, FASTQ and extract sequence IDs belonging to user supplied taxa name of interest." version="0.1.0" python_template_version="3.5"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="3.9">python</requirement> | |
| 4 <requirement type="package">biopython</requirement> | |
| 5 <requirement type="package">pandas</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t '$output1' | |
| 9 ]]></command> | |
| 10 <inputs> | |
| 11 <param type="data" name="input1" format="txt" /> | |
| 12 <param type="data" name="input2" format="txt" /> | |
| 13 <param type="text" name="input3" format="txt" /> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data name="output1" format="txt" /> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="input1" value="FAL11127.centrifuge.output.txt"/> | |
| 21 <param name="input2" value="FAL11127.centrifuge.report.txt"/> | |
| 22 <param name="input3" value="Escherichia coli"/> | |
| 23 <output name="output1" file="FAL11127.process-centrifuge-bug-ids.txt"/> | |
| 24 </test> | |
| 25 </tests> | |
| 26 <help><![CDATA[ | |
| 27 usage: process_centrifuge_output.py [-h] [-v] [-i INPUT_FASTQ] -t TAXA_FILTERED_FASTQ_FILE -r CENT_REPORT -o | |
| 28 CENT_OUTPUT -b BUG | |
| 29 | |
| 30 This script is part of the centriflaken pipeline: It processes centrifuge output and produces either a filtered FASTQ | |
| 31 or a text file of FASTQ IDs based on the supplied taxa/bug | |
| 32 | |
| 33 optional arguments: | |
| 34 -h, --help show this help message and exit | |
| 35 -v For more verbose output | |
| 36 -i INPUT_FASTQ Path to input FASTQ file (same as input to centrifuge). If not mentioned, a text file of | |
| 37 sequence IDs are produced instead of a FASTQ file | |
| 38 -t TAXA_FILTERED_FASTQ_FILE | |
| 39 Path to output FASTQ or output text file filtered by the taxa specified | |
| 40 -r CENT_REPORT Path to centrifuge report | |
| 41 -o CENT_OUTPUT Path to centrifuge output | |
| 42 -b BUG Name or fragment of name of the bug by which reads are extracted | |
| 43 ]]></help> | |
| 44 <citations> | |
| 45 <citation type="bibtex"> | |
| 46 @misc{gitlabcpipescentriflaken, | |
| 47 author = {Konganti, Kranti}, | |
| 48 year = {2022}, | |
| 49 title = {CPIPES}, | |
| 50 publisher = {GitLab}, | |
| 51 journal = {GitLab repository}, | |
| 52 url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes}, | |
| 53 }</citation> | |
| 54 </citations> | |
| 55 </tool> |