Mercurial > repos > alenail > map_to_known_genes
comparison map_to_known_genes/map_to_known_genes.xml @ 0:3f12a2b0af50 draft default tip
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author | alenail |
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date | Thu, 14 Apr 2016 11:34:47 -0400 |
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-1:000000000000 | 0:3f12a2b0af50 |
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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 $tss | |
13 --peaks-format=$peaks_fmt | |
14 --upstream-window=$upst_win | |
15 --downstream-window=$dnst_win | |
16 --map-output="$peaksOutput" | |
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 | |
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" /> | |
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" /> | |
29 | |
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="" /> | |
31 | |
32 <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false"> | |
33 <option value="MACS">MACS</option> | |
34 <option selected="true" value="BED">BED</option> | |
35 </param> | |
36 | |
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="" /> | |
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="" /> | |
39 </inputs> | |
40 <outputs> | |
41 <data name="peaksOutput" format="txt" hidden="false" /> | |
42 </outputs> | |
43 <help></help> | |
44 </tool> |