Mercurial > repos > mingchen0919 > deseq2_rmarkdown
changeset 6:f1e4bfc58975 draft
Uploaded
| author | mingchen0919 |
|---|---|
| date | Mon, 07 Aug 2017 18:11:38 -0400 |
| parents | 507e408cd6cc |
| children | a5fdd120b2c7 |
| files | DESeq_visualization.xml |
| diffstat | 1 files changed, 95 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DESeq_visualization.xml Mon Aug 07 18:11:38 2017 -0400 @@ -0,0 +1,95 @@ +<tool id="DESeq_visualization" name="DESeq2: Visualization" 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> + </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[ + ## Add tools to PATH + export PATH=/opt/R-3.2.5/bin:\$PATH && + + 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> +</tool> \ No newline at end of file