Mercurial > repos > ning > ebseq
view EBGeneTwoCondTest.xml @ 25:b729d890413b draft
Uploaded
author | ning |
---|---|
date | Mon, 16 Jun 2014 12:31:02 -0400 |
parents | b6465cb90cc0 |
children |
line wrap: on
line source
<tool id="EBGeneTwoCondTest" name="Gene level DE test across two conditions"> <description>Runs EBSeq to find DE genes across two conditions</description> <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBGeneTwoCondTest.R --args $Gene_Expression $First_Row_Sample_Names $Conditions $Target_FDR $Output $Sorted_Output $Sorted_Output_with_target_FDR $Sizes</command> <inputs> <param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab delimited, please use the unnormalized values, e.g. expected counts form RSEM)"/> <param name="First_Row_Sample_Names" type="select" format="text"> <label>The First Row is Sample Names?</label> <option value="y">Yes</option> <option value="n">No</option> </param> <param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each sample belongs to (separated by comma, no space please)." help=""/> <param name="Target_FDR" type="text" format="tabular" value="0.05" label="Target FDR" /> </inputs> <outputs> <data format="tabular" name="Output" /> <data format="tabular" name="Sorted_Output" /> <data format="tabular" name="Sorted_Output_with_target_FDR" /> <data format="tabular" name="Sizes" /> </outputs> <help> The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of columns in the data file (except the gene names column). Four output files will be generated. Each of the first 3 files contains Posterior probability of being DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized gene expressions. The Four files are: Genes with the same order as in input file; Genes sorted by PPDE; DE Genes under target FDR (PPDE>=TargetFDR) and sorted by PPDE; Library size factor for each sample. </help> </tool>