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