Mercurial > repos > mingchen0919 > rmarkdown_deseq2_test
diff DESeq_visualization.xml @ 0:61c184384d02 draft default tip
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2
| author | mingchen0919 |
|---|---|
| date | Tue, 07 Nov 2017 10:02:57 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DESeq_visualization.xml Tue Nov 07 10:02:57 2017 -0500 @@ -0,0 +1,145 @@ +<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> \ No newline at end of file