Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
view DiffExpAnal/deseq.xml @ 6:59cc55f611f6 draft
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author | yufei-luo |
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date | Tue, 22 Jan 2013 10:46:42 -0500 |
parents | 63799b789162 |
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<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>