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1 <tool id="statonlab_fasta_splitter" name="statonlab_fasta_splitter" version="1.0.0">
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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>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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8 <requirement type="package" version="5.22.2.1">perl</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="XXX" source="stderr" level="warning"
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12 description="Check the warnings_and_errors.txt file for more details."/>
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13 </stdio>
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14 <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
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15
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16 Rscript '${__tool_directory__}/'split_fasta_render.R
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17
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18 -o '$report'
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19 -d '$report.files_path'
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20 -s '$sink_message'
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21 -A '$fasta_input'
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22 -B '$number'
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23 ]]></command>
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24 <inputs>
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25 <param type="data" name="fasta_input" label="FASTA input" optional="False" multiple="False"/>
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26 <param type="integer" name="number" label="Number" help="The number of files the FASTA file will be split into"
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27 optional="False" value="200" min="1"/>
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28 </inputs>
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29 <outputs>
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30 <data format="html" name="report" label="tool report"/>
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31 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
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32 <collection name="list_collection" type="list" label="${tool.name} on ${on_string}">
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33 <discover_datasets pattern="__name_and_ext__" directory="fasta_files" visible="true"/>
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34 </collection>
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35 </outputs>
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36 <citations>
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37 <citation type="bibtex"><![CDATA[
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38 @article{allaire2016rmarkdown,
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39 title={rmarkdown: Dynamic Documents for R, 2016},
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40 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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41 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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42 journal={R package version 0.9},
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43 volume={6},
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44 year={2016}
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45 }
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46 ]]></citation>
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47 <citation type="bibtex"><![CDATA[
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48 @book{xie2015dynamic,
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49 title={Dynamic Documents with R and knitr},
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50 author={Xie, Yihui},
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51 volume={29},
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52 year={2015},
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53 publisher={CRC Press}
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54 }
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55 ]]></citation>
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56 </citations>
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57 </tool>
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