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<tool id="macs" name="MACS"> <description>Model-based Analysis of ChiP-Seq</description> <command interpreter="python"> macs_wrapper.py -t $mappedReadsIP -c $mappedReadsControl --name $experimentName --format $inputFormat['formatSelect'] --gsize $genomeSize --tsize $tagLength --bw $bandWidth --pvalue $pValueCutoff --mfold $hcEnrichmentRatio --shiftsize $shiftSize --peaks-xls $peaksXLS --peaks-bed $peaksBED --neg-peaks-xls $negPeaksXLS --neg-peaks-bed $negPeaksBED --R-model $rModel </command> <inputs> <conditional name="inputFormat"> <param name="formatSelect"> <option value="BED">BED</option> <option value="ELAND" selected="true">ELAND</option> </param> <when value="BED"> <param type="data" format="BED" name="mappedReadsIP" label="Mapped reads file from IP"/> <param type="data" format="BED" name="mappedReadsControllabel="Mapped reads file from control"/> </when> <when value="ELAND"> <param type="data" format="ELAND" name="mappedReadsIP" label="Mapped reads file from IP"/> <param type="data" format="ELAND" name="mappedReadsControl" label="Mapped reads file from control"/> </when> </conditional> <param type="text" name="experimentName" label="Experiment name" /> <param name="genomeSize" type="integer" label="Genome size"/> <param name="tagLength" type="integer" value="25" label="Tag length" /> <param name="bandWidth" type="integer" value="300" label="Band width" /> <param name="pValueCutoff" type="float" value=".00001" label="Pvalue cutoff" /> <param name="hcEnrichmentRatio" type="integer" value="32" label="High-confidence enrichment ratio" /> <param name="shiftSize" type="integer" value="100" label="Shift size in bp" /> </inputs> <outputs> <data format="xls" name="peaksXLS" label="Called peaks (xls)"/> <data format="bed" name="peaksBED" label="Called peaks (bed)"/> <data format="xls" name="negPeaksXLS" label="Negative peaks (xls)"/> <data format="bed" name="negPeaksBED" label="Negative peaks (bed)"/> <data format="text" name="rModel" label="R script for generating model pdf"/> </outputs> </tool>
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