kkonganti@0: <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">
kkonganti@0:     <requirements>
kkonganti@0:         <requirement type="package" version="3.9">python</requirement>
kkonganti@0:         <requirement type="package">biopython</requirement>
kkonganti@0:         <requirement type="package">pandas</requirement>
kkonganti@0:     </requirements>
kkonganti@0:     <command detect_errors="exit_code"><![CDATA[
kkonganti@0:         $__tool_directory__/process_centrifuge_output.py -o '$input1' -r '$input2' -b '$input3' -t '$output1'
kkonganti@0:     ]]></command>
kkonganti@0:     <inputs>
kkonganti@0:         <param type="data" name="input1" format="txt" />
kkonganti@0: 	<param type="data" name="input2" format="txt" />
kkonganti@0: 	<param type="text" name="input3" format="txt" />
kkonganti@0:     </inputs>
kkonganti@0:     <outputs>
kkonganti@0:         <data name="output1" format="txt" />
kkonganti@0:     </outputs>
kkonganti@0:     <tests>
kkonganti@0:         <test>
kkonganti@0:             <param name="input1" value="FAL11127.centrifuge.output.txt"/>
kkonganti@0: 	    <param name="input2" value="FAL11127.centrifuge.report.txt"/>
kkonganti@0: 	    <param name="input3" value="Escherichia coli"/>
kkonganti@0:             <output name="output1" file="FAL11127.process-centrifuge-bug-ids.txt"/>
kkonganti@0:         </test>
kkonganti@0:     </tests>
kkonganti@0:     <help><![CDATA[
kkonganti@0: usage: process_centrifuge_output.py [-h] [-v] [-i INPUT_FASTQ] -t TAXA_FILTERED_FASTQ_FILE -r CENT_REPORT -o
kkonganti@0:                                     CENT_OUTPUT -b BUG
kkonganti@0: 
kkonganti@0: This script is part of the centriflaken pipeline: It processes centrifuge output and produces either a filtered FASTQ
kkonganti@0: or a text file of FASTQ IDs based on the supplied taxa/bug
kkonganti@0: 
kkonganti@0: optional arguments:
kkonganti@0:   -h, --help            show this help message and exit
kkonganti@0:   -v                    For more verbose output
kkonganti@0:   -i INPUT_FASTQ        Path to input FASTQ file (same as input to centrifuge). If not mentioned, a text file of
kkonganti@0:                         sequence IDs are produced instead of a FASTQ file
kkonganti@0:   -t TAXA_FILTERED_FASTQ_FILE
kkonganti@0:                         Path to output FASTQ or output text file filtered by the taxa specified
kkonganti@0:   -r CENT_REPORT        Path to centrifuge report
kkonganti@0:   -o CENT_OUTPUT        Path to centrifuge output
kkonganti@0:   -b BUG                Name or fragment of name of the bug by which reads are extracted
kkonganti@0:     ]]></help>
kkonganti@0:     <citations>
kkonganti@0:         <citation type="bibtex">
kkonganti@0: @misc{gitlabcpipescentriflaken,
kkonganti@0:   author = {Konganti, Kranti},
kkonganti@0:   year = {2022},
kkonganti@0:   title = {CPIPES},
kkonganti@0:   publisher = {GitLab},
kkonganti@0:   journal = {GitLab repository},
kkonganti@0:   url = {https://cfsan-git.fda.gov/Kranti.Konganti/cpipes},
kkonganti@0: }</citation>
kkonganti@0:     </citations>	
kkonganti@0: </tool>