Mercurial > repos > mingchen0919 > aurora_dustmasker
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author | mingchen0919 |
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date | Fri, 09 Nov 2018 15:25:01 -0500 |
parents | b8c76b06d724 |
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<tool id="aurora_dustmasker" name="aurora_dustmasker" version="1.0.0"> <description>Low complexity region masker based on Symmetric DUST algorithm</description> <requirements> <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> <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it. mkdir -p $report.files_path && ######### three important paths: ######### 1. path to tool installation directory ######### 2. path to report html ######### 3. path to files_path directory associated with the report output. export TOOL_INSTALL_DIR='${__tool_directory__}' && export REPORT='$report' && export REPORT_FILES_PATH='$report.files_path' && ############ create a hidden file to store r markdown rendering log touch $report.files_path/r_rendering.log.txt && ############ finally run the render.R script Rscript '${__tool_directory__}/rmarkdown_report_render.R' -o $report -d $report.files_path -A $input_fasta -B $window_length -C $level -D $linker -E $input_format -F $output_format -G $parse_seqids -H $out ]]></command> <inputs> <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="fasta" selected="true">fasta</option><option value="blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="acclist" selected="false">acclist</option><option value="fasta" selected="true">fasta</option><option value="interval" selected="false">interval</option><option value="maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="maskinfo_xml" selected="false">maskinfo_xml</option><option value="seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs> <outputs> <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" format="fasta" label="${tool.name} on ${on_string}" hidden="false"/></outputs> <citations> <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown, title={rmarkdown: Dynamic Documents for R, 2016}, author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, journal={R package version 0.9}, volume={6}, year={2016} } ]]></citation><citation type="bibtex"><![CDATA[ @book{xie2015dynamic, title={Dynamic Documents with R and knitr}, author={Xie, Yihui}, volume={29}, year={2015}, publisher={CRC Press} } ]]></citation><citation type="bibtex"><![CDATA[ @online{jstree, author={Bozhanov, Ivan}, year = 2018, url = {https://www.jstree.com/} } ]]></citation></citations> </tool>