Mercurial > repos > mingchen0919 > rmarkdown_wgcna
view wgcna_eigengene_visualization.xml @ 6:05bcad4b5b4f draft default tip
minor fix function missing issue
author | mingchen0919 |
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date | Sun, 26 Nov 2017 11:04:08 -0500 |
parents | a1a34771304e |
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<tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.2"> <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="1.3">r-rmarkdown</requirement> <requirement type="package" version="1.8.4">r-plyr</requirement> <requirement type="package" version="0.2">r-dt</requirement> <requirement type="package" version="0.3.5">r-htmltools</requirement> <requirement type="package" version="1.51">r-wgcna</requirement> </requirements> <description> Eigengene visualization. </description> <stdio> <regex match="Execution halted" source="both" level="fatal" description="Execution halted." /> <regex match="Error in" source="both" level="fatal" description="An undefined error occured, please check your intput carefully and contact your administrator." /> <regex match="Fatal error" source="both" level="fatal" description="An undefined error occured, please check your intput carefully and contact your administrator." /> </stdio> <command> <![CDATA[ ## Add tools to PATH export PATH=/opt/R-3.2.5/bin:\$PATH && Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R' ## 1. input data -e $echo -w $construct_network_workspace -p '$soft_threshold_power' -n $plot_genes ## 2. output report and report site directory -o $wgcna_eigengene_visualization -d $wgcna_eigengene_visualization.files_path ## 3. Rmd templates in the tool directory -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd' ]]> </command> <inputs> <param type="data" name="construct_network_workspace" format="rdata" optional="false" label="R workspace from WGCNA: construct network" /> <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power" help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power. An optimal power will be calculated automatically if no value is provided." /> <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false" help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." /> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> </inputs> <outputs> <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" /> </outputs> <citations> <citation type="bibtex"> @article{langfelder2008wgcna, title={WGCNA: an R package for weighted correlation network analysis}, author={Langfelder, Peter and Horvath, Steve}, journal={BMC bioinformatics}, volume={9}, number={1}, pages={559}, year={2008}, publisher={BioMed Central} } </citation> <citation type="bibtex"> @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"> @book{xie2015dynamic, title={Dynamic Documents with R and knitr}, author={Xie, Yihui}, volume={29}, year={2015}, publisher={CRC Press} } </citation> <citation> @misc{dt2016, title = {DT: A Wrapper of the JavaScript Library 'DataTables'}, author = {Yihui Xie}, year = {2016}, note = {R package version 0.2}, url = {https://CRAN.R-project.org/package=DT}, } </citation> </citations> </tool>