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1 <tool id="chipsequtil_maptoknowngenes" name="Map Peaks to Known Genes" version="0.1">
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2 <description>
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3 Map the peaks in <peaks file> to genes in <knownGene file>. <knownGene file> isformat is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.<peaks file> format is as produced by MACS. If *auto* is chosen (default) file extension is examined for *.xls* for default MACS format or *.bed* for BED format. If the --detail option is provided, the following extra fields are appended to each row:
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4 peak loc, dist from feature, map type, map subtype
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5 </description>
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6 <parallelism method="basic"></parallelism>
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7 <requirements>
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8 <requirement type="package" version="1.0">chipsequtil</requirement>
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9 </requirements>
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10 <command interpreter="python">
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11 map_to_known_genes.py
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12 $tss
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13 --peaks-format=$peaks_fmt
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14 --upstream-window=$upst_win
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15 --downstream-window=$dnst_win
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16 --map-output="$peaksOutput"
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17 $detail
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18 $intergenic
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19 $knownGeneFile $knownGeneRef $macsPeaksFile
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20
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21 </command>
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22 <inputs>
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23 <param name="knownGeneFile" type="data" label="knownGene file" help="" optional="false" />
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24 <param name="knownGeneRef" type="data" label="knownGene xRef file" help="" optional="false" />
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25 <param name="macsPeaksFile" type="data" label="Peaks File" help="" optional="false" />
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26
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27 <param name="upst_win" type="integer" label="Upstream Window" help="Window width in base pairs to consider promoter region [default: %default]" optional="false" value="5500" />
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28 <param name="dnst_win" type="integer" label="Downstream Window" help="Window width in base pairs to consider downstream region [default: %default]" optional="false" value="2500" />
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29
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30 <param name="tss" checked="true" label="Calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" />
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31
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32 <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false">
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33 <option value="MACS">MACS</option>
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34 <option selected="true" value="BED">BED</option>
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35 </param>
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36
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37 <param name="detail" checked="true" label="Append the following fields to each row: peak loc, dist from feature, map type, map subtype" type="boolean" truevalue="--detail" falsevalue="" help="" />
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38 <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" />
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39 </inputs>
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40 <outputs>
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41 <data name="peaksOutput" format="txt" hidden="false" />
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42 </outputs>
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43 <help></help>
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44 </tool>
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