Mercurial > repos > mingchen0919 > rmarkdown_deseq2
view DESeq_visualization.xml @ 5:fd3514267506 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 15:06:40 -0400 |
parents | 7f0281d26b81 |
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<tool id="DESeq_visualization" name="DESeq2: Visualization" version="1.0.0"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.2">r-rmarkdown</requirement> <requirement type="package" version="1.8.4">r-plyr</requirement> <requirement type="package" version="1.1.0">r-stringr</requirement> <requirement type="package" version="0.4.0">r-highcharter</requirement> <requirement type="package" version="0.2">r-dt</requirement> <requirement type="package" version="1.4.2">r-reshape2</requirement> <requirement type="package" version="4.5.6">r-plotly</requirement> <requirement type="package" version="0.2.0.1">r-formattable</requirement> <requirement type="package" version="0.3.5">r-htmltools</requirement> <requirement type="package" version="1.0.8">r-pheatmap</requirement> </requirements> <description> An R Markdown tool to visualize DESeq analysis results. </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[ Rscript '${__tool_directory__}/DESeq_visualization_render.R' ## 1. input data -e $echo -w $deseq_workspace #set $pca_groups = [] #for $group in $intgroups_pca #if str($group.intgroup) #set $pca_groups = $pca_groups + [str($group.intgroup)] #end if #end for #set $pca_groups = ','.join($pca_groups) -p "$pca_groups" #set $mds_groups = [] #for $group in $intgroups_mds #if str($group.intgroup) #set $mds_groups = $mds_groups + [str($group.intgroup)] #end if #end for #set $mds_groups = ','.join($mds_groups) -m "$mds_groups" ## 2. output report and report site directory -o $deseq_visualization -d $deseq_visualization.files_path ## 3. Rmd templates sitting in the tool directory ## _site.yml and index.Rmd template files -D '${__tool_directory__}/DESeq_visualization.Rmd' ]]> </command> <inputs> <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" /> <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" /> <repeat name="intgroups_pca" title="Interest groups for PCA plot" min="1"> <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true" optional="false" label="Interest group for PCA plot" help=""/> </repeat> <repeat name="intgroups_mds" title="Interest groups for MDS plot" min="1"> <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true" optional="false" label="Interest group for MDS plot" help=""/> </repeat> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> </inputs> <outputs> <data name="deseq_visualization" format="html" label="DESeq Visualization" /> </outputs> <citations> <citation> @article{love2014moderated, title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}, author={Love, Michael I and Huber, Wolfgang and Anders, Simon}, journal={Genome biology}, volume={15}, number={12}, pages={550}, year={2014}, 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{pheatmap2015, title = {pheatmap: Pretty Heatmaps}, author = {Raivo Kolde}, year = {2015}, note = {R package version 1.0.8}, url = {https://CRAN.R-project.org/package=pheatmap}, } </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>