Mercurial > repos > mingchen0919 > rmarkdown_deseq2
view DESeq_results.xml @ 0:7231d7e8d3ed draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 10:43:18 -0400 |
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children | 15a5fb1a2ac8 |
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<tool id="DESeq_results" name="DESeq2: Results" version="1.0.0"> <requirements> <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 display DESeq analysis. </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_results_render.R' ## 1. input data -e $echo -w $deseq_workspace -c "$contrast_group" -t $treatment -k $condition #set $groups = [] #for $c_group in $clustering_groups #if str($c_group.group) #set $groups = $groups + [str($c_group.group)] #end if #end for #set $groups = ','.join($groups) -m "$groups" ## 2. output report and report site directory -o $deseq_results -d $deseq_results.files_path ## 3. Rmd templates sitting in the tool directory ## _site.yml and index.Rmd template files -D '${__tool_directory__}/DESeq_results.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" /> <param type="data_column" name="contrast_group" data_ref="sample_table" use_header_names="true" optional="false" label="Group for result contrast" help=""/> <param type="text" name="treatment" label="Treatment level" /> <param type="text" name="condition" label="Condition level" /> <repeat name="clustering_groups" title="Gene clustering groups" min="1"> <param type="data_column" name="group" data_ref="sample_table" use_header_names="true" optional="false" label="A phenotype column from the sample table" /> </repeat> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> </inputs> <outputs> <data name="deseq_results" format="html" label="DESeq Results" /> </outputs> </tool>