Mercurial > repos > mingchen0919 > aurora_deseq2_site
diff rmarkdown_report.xml @ 1:32210899a3dd draft
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
| author | mingchen0919 |
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| date | Sun, 30 Dec 2018 12:45:56 -0500 |
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| children | ab8d558ea6e6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report.xml Sun Dec 30 12:45:56 2018 -0500 @@ -0,0 +1,131 @@ +<tool name="aurora_deseq2_site" id='aurora_deseq2_site_report' version="2.2.1"> + <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> + </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 $report.files_path + -A '$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="data" name="count_data" label="Count data" + help="The first column is sample names; The remaining columns are read counts from each sample." + optional="False" format="csv"/> + <param type="data" name="column_data" label="Column data" + help="The first column are sample names (column name from the count 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="${tool.name} on ${on_string}"/> + <data name="significant_genes" format="tabular" label="${tool.name} signficant genes 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> + <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>