Mercurial > repos > mingchen0919 > aurora_deseq2_site
diff DESeq.xml @ 0:6f94b4b9de44 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 23:57:53 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DESeq.xml Tue Feb 27 23:57:53 2018 -0500 @@ -0,0 +1,106 @@ +<tool name="DESeq2: Analysis" id='deseq2' version="2.0.1"> + <description> + perform differential expression analysis + </description> + <requirements> + <requirement type="package" version="1.15.0.6-0">pandoc</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="1.6">r-rmarkdown</requirement> + <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> + <requirement type="package" version="0.2">r-dt</requirement> + <requirement type="package" version="1.0.8">r-pheatmap</requirement> + </requirements> + <stdio> + <regex match="XXX" source="stderr" level="warning" + description="Check the warnings_and_errors.txt file for more details."/> + </stdio> + <command><![CDATA[ + + + Rscript '${__tool_directory__}/DESeq_render.R' + + -e $echo + + -o $report + -d $report.files_path + -s $sink_message + -t '${__tool_directory__}' + + + ##----- code chunk to get file paths and raw file names for a multiple inputs data field ---- + #set $sep = '' + #set $count_file_paths = '' + #set $count_file_names = '' + #for $count_file in $count_files: + #set $count_file_paths += $sep + str($count_file) + #set $count_file_names += $sep + str($count_file.name) + #set $sep = ',' + #end for + ##----------------- end for getting file names and file paths ------------------------------ + -P '$count_file_paths' + -N '$count_file_names' + -S $sample_table + -p '$design_formula' + -w $deseq_workspace + + + ]]></command> + <inputs> + <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" + label="Display analysis code in report?"/> + <param type="data" name="count_files" format="txt" multiple="true" label="Count files from htseq-count"/> + <param type="data" name="sample_table" format="txt" multiple="false" label="sample table file" + help="The sample table file contains a table. The first column is the sample name, the second column is + the count file name and the rest of columns are treatment columns. The file names in this table have + to be in the same order as the count files uploaded in the previous step. "/> + <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula" + help="The simplest design formula for differential expression would be ~ condition, where condition + is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value="~"/> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data name="report" format="html" label="DESeq Analysis on ${on_string}"/> + <data format="txt" name="sink_message" label="Warnings and Errors on" + from_work_dir="warnings_and_errors.txt"/> + <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/> + </outputs> + <citations> + <citation type="bibtex"> + @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"><![CDATA[ + @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"><![CDATA[ + @book{xie2015dynamic, + title={Dynamic Documents with R and knitr}, + author={Xie, Yihui}, + volume={29}, + year={2015}, + publisher={CRC Press} + } + ]]></citation> + </citations> +</tool>