Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
diff DiffExpAnal/deseq.xml @ 0:63799b789162 draft
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| author | yufei-luo |
|---|---|
| date | Tue, 22 Jan 2013 10:07:03 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DiffExpAnal/deseq.xml Tue Jan 22 10:07:03 2013 -0500 @@ -0,0 +1,28 @@ +<tool id="DESEQ" name="DESEQ for differential expression analysis"> + <description>Differential expression analysis for reads count data</description> + <requirements> + <requirement type="package">R</requirement> + <requirement type="package">Biobase</requirement> + <requirement type="package">DESeq</requirement> + </requirements> + + <command interpreter="bash"> deseq.sh $inputFile $header $withOutReplicates $outHTML $outHTML.files_path $outComplete $outUP $outDown 2> $log </command> + + <inputs> + <param name="inputFile" type="data" label="Input File list" format="txt"/> + <param name="header" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If there is a header for your count files, please choose this case."/> + <param name="withOutReplicates" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If your data has not replicates, please choose this case."/> + + </inputs> + + <outputs> + <data format="HTML" name="outHTML" label="[DESEQ] Output HTML File" help="This output file shows all results images by DESeq analysis"/> + <data format="tabular" name="outComplete" label="[DESEQ] Output complete File"/> + <data format="tabular" name="outUP" label="[DESEQ] Output up File" help="This output file shows the genes of group1 which are overexpressed than those of group2"/> + <data format="tabular" name="outDown" label="[DESEQ] Output down File" help="This output file shows the genes of group1 which are less expressed than those of group2"/> + <data format="txt" name="log" label="[DESEQ] Output log File"/> + </outputs> + + <help> + </help> +</tool>