Mercurial > repos > alenail > chipsequtil
comparison chipsequtil/map_to_known_genes.xml @ 0:4f66143b385a draft
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author | alenail |
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date | Mon, 28 Mar 2016 13:08:59 -0400 |
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children | 0eaa8225a09a |
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-1:000000000000 | 0:4f66143b385a |
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1 <tool id="chipsequtil_maptoknowngenes" name="Map Peaks to Known Genes" version="0.1"> | |
2 <description> | |
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: | |
4 peak loc, dist from feature, map type, map subtype | |
5 </description> | |
6 <parallelism method="basic"></parallelism> | |
7 <requirements> | |
8 <requirement type="package" version="1.0">chipsequtil</requirement> | |
9 </requirements> | |
10 <command interpreter="python"> | |
11 map_to_known_genes.py | |
12 $tss | |
13 --upstream-window=$upst_win | |
14 --downstream-window=$dnst_win | |
15 --map-output=$peaksOutput | |
16 --peaks-format=$peaks_fmt | |
17 $detail | |
18 $intergenic | |
19 $knownGeneFile $knownGeneRef $macsPeaksFile | |
20 | |
21 </command> | |
22 <inputs> | |
23 <param name="knownGeneFile" type="data" label="knownGene file" help="" optional="false" /> | |
24 <param name="knownGeneRef" type="data" label="knownGene xRef file" help="" optional="false" /> | |
25 <param name="macsPeaksFile" type="data" label="Peaks File" help="" optional="false" /> | |
26 <param name="peaksOutput" type="text" label="Output filename" help="filename to output mapped peaks to" optional="false" /> | |
27 | |
28 <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" /> | |
29 <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" /> | |
30 | |
31 <param name="tss" checked="true" label="calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" /> | |
32 | |
33 <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false"> | |
34 <option value="auto">auto</option> | |
35 <option value="MACS">MACS</option> | |
36 <option selected="true" value="BED">BED</option> | |
37 </param> | |
38 | |
39 <param name="detail" checked="false" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" /> | |
40 <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="" /> | |
41 </inputs> | |
42 <outputs> | |
43 <data format="txt" hidden="false" name="default"/> | |
44 </outputs> | |
45 <help></help> | |
46 </tool> |