Mercurial > repos > mingchen0919 > aurora_deseq2_site
view deseq2_site.xml @ 3:1faa864c0839 draft
update 2.2.0
author | mingchen0919 |
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date | Fri, 09 Mar 2018 09:06:06 -0500 |
parents | 706ecfe0bac3 |
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<tool id="aurora_deseq2_site" name="Aurora DESeq2 site" version="2.2.0"> <description>Differential analysis of count data with the DESeq2 package</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="1.14.1">bioconductor-deseq2</requirement> <requirement type="package" version="4.5.6">r-plotly</requirement> <requirement type="package" version="2.2.1">r-ggplot2</requirement> <requirement type="package" version="1.0.8">r-pheatmap</requirement> <requirement type="package" version="0.2">r-dt</requirement> </requirements> <stdio> <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/> </stdio> <command><![CDATA[Rscript '${__tool_directory__}/deseq2_site_render.R' -e $echo -o $report -d $report.files_path -s $sink_message -t '${__tool_directory__}' -A '$count_data' -B '$column_data' -C '$design_formula' -D '$treatment_name' -E '$treated' -F '$untreated' -G '$test_type' -H '$fit_type' -I '$alpha' -J '$significant_genes']]></command> <inputs> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Display analysis code in report?"/> <param type="data" name="count_data" label="Count data" help="an RData file that stores the count matrix data. The file is generated from the aurora_htseq tool." optional="False" format="rdata"/> <param type="data" name="column_data" label="Column data" help="A table file that stores column data for DESeq2 analysis. The first columns are the column names from the count matrix data. The remaining columns are experimental treatments." optional="False" format="csv"/> <param type="text" name="design_formula" label="Design formula" help="The design formula expresses the variables which will be used in modeling. The formula should be a tilde (~) followed by the variables with plus signs between them, e.g., ~ condition1 + condition2" optional="False"> <sanitizer sanitize="true"> <valid initial="default"> <add preset="string.printable"/> <add value="~"/> </valid> </sanitizer> </param> <param type="text" name="treatment_name" label="Treatment name" help="one of the treatment column names from the column data." optional="False"/> <param type="text" name="treated" label="Treated" help="A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis." optional="False"/> <param type="text" name="untreated" label="Untreated" help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis." optional="False"/> <param type="select" name="test_type" label="Test type" optional="False"> <option value="Wald" selected="true">Wald</option> <option value="LRT" selected="false">Likelihood Ratio Test (LRT)</option> </param> <param type="select" name="fit_type" label="Fitting of dispersions" help="either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity" optional="False"> <option value="parametric" selected="true">parametric</option> <option value="local" selected="false">local</option> <option value="mean" selected="false">mean</option> </param> <param type="float" name="alpha" label="Alpha" help="the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value." optional="False" value="0.1" min="0" max="1"/> </inputs> <outputs> <data format="html" name="report" label="Aurora DESeq2 site"/> <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/> <data name="significant_genes" format="csv" label="signficant genes from ${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[@article{love2014differential, title={Differential analysis of count data--the DESeq2 package}, author={Love, Michael and Anders, Simon and Huber, Wolfgang}, journal={Genome Biol}, volume={15}, pages={550}, year={2014} }]]></citation> </citations> </tool>