Mercurial > repos > mingchen0919 > rmarkdown_deseq2
diff 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 |
parents | |
children | 15a5fb1a2ac8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DESeq_results.xml Tue Aug 08 10:43:18 2017 -0400 @@ -0,0 +1,88 @@ +<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> \ No newline at end of file