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1
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1 <tool id="split_multifasta" name="split_multifasta" version="1.0.0">
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0
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2 <description>Split a single FASTA file into multiple smaller FASTA files
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="5.22.2.1">perl</requirement></requirements>
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6 <stdio>
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7 <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
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8 <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
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9
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10 Rscript '${__tool_directory__}/'split_fasta_render.R
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11
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12 -o '$report'
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13 -d '$report.files_path'
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14 -s '$sink_message'
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15 -A '$fasta_input'
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16 -B '$number'
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17 ]]></command>
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18 <inputs>
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19 <param type="data" name="fasta_input" label="FASTA input" optional="False" multiple="False"/><param type="integer" name="number" label="Number" help="The number of files the FASTA file will be split into" optional="False" value="200" min="1"/></inputs>
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20 <outputs>
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21 <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/><data name="sink_message" format="txt" label="log on ${on_string}" from_work_dir="warnings_and_errors.txt" hidden="false"/><collection name="list_collection" type="list" label="${tool.name} on ${on_string}"><discover_datasets pattern="__name_and_ext__" directory="fasta_files" visible="true"/></collection></outputs>
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22 <citations>
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23 <citation type="bibtex"><![CDATA[
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24 @article{allaire2016rmarkdown,
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25 title={rmarkdown: Dynamic Documents for R, 2016},
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26 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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27 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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28 journal={R package version 0.9},
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29 volume={6},
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30 year={2016}
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31 }
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32 ]]></citation><citation type="bibtex"><![CDATA[
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33 @book{xie2015dynamic,
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34 title={Dynamic Documents with R and knitr},
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35 author={Xie, Yihui},
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36 volume={29},
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37 year={2015},
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38 publisher={CRC Press}
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39 }
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40 ]]></citation></citations>
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41 </tool>
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