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1 <tool id="aurora_dustmasker" name="aurora_dustmasker" version="1.0.0">
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2 <description>Low complexity region masker based on Symmetric DUST algorithm</description>
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3 <requirements>
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4 <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="2.7.1">blast</requirement></requirements>
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5 <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it.
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6 mkdir -p $report.files_path &&
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7
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8 ######### three important paths:
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9 ######### 1. path to tool installation directory
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10 ######### 2. path to report html
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11 ######### 3. path to files_path directory associated with the report output.
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12 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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13 export REPORT='$report' &&
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14 export REPORT_FILES_PATH='$report.files_path' &&
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15
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16 ############ create a hidden file to store r markdown rendering log
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17 touch $report.files_path/r_rendering.log.txt &&
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18
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19 ############ finally run the render.R script
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20 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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21
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22 -o $report
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23 -d $report.files_path
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24
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25 -A $input_fasta
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26 -B $level
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27 -C $linker
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28 -D $input_format
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29 -E $output_format
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30 -F $parse_seqids
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31
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32 -G $out
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33
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34
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35 ]]></command>
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36 <inputs>
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37 <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="input_format_fasta" selected="true">fasta</option><option value="input_format_blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="output_acclist" selected="false">acclist</option><option value="output_fasta" selected="false">fasta</option><option value="output_interval" selected="false">interval</option><option value="output_maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="output_maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="output_maskinfo_xml" selected="false">maskinfo_xml</option><option value="output_seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="output_seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="output_seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs>
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38 <outputs>
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39 <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" label="${tool.name} on ${on_string}" hidden="false"/></outputs>
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40 <citations>
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41 <citation type="bibtex"><![CDATA[
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42 @article{allaire2016rmarkdown,
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43 title={rmarkdown: Dynamic Documents for R, 2016},
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44 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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45 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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46 journal={R package version 0.9},
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47 volume={6},
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48 year={2016}
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49 }
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50 ]]></citation><citation type="bibtex"><![CDATA[
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51 @book{xie2015dynamic,
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52 title={Dynamic Documents with R and knitr},
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53 author={Xie, Yihui},
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54 volume={29},
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55 year={2015},
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56 publisher={CRC Press}
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57 }
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58 ]]></citation><citation type="bibtex"><![CDATA[
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59 @online{jstree,
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60 author={Bozhanov, Ivan},
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61 year = 2018,
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62 url = {https://www.jstree.com/}
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63 }
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64 ]]></citation></citations>
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65 </tool>
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