Mercurial > repos > alenail > chipsequtil

comparison chipsequtil/map_to_known_genes.xml @ 6:124231ed2402 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author alenail
date Mon, 04 Apr 2016 14:56:51 -0400
parents 0eaa8225a09a
children a30aa2806375
comparison
equal deleted inserted replaced
5:199989365def 6:124231ed2402
26 <param name="peaksOutput" type="text" label="Output filename" help="filename to output mapped peaks to" optional="false" /> 26 <param name="peaksOutput" type="text" label="Output filename" help="filename to output mapped peaks to" optional="false" />
27 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" /> 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" /> 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 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="" /> 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 32
33 <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false"> 33 <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false">
34 <option value="MACS">MACS</option> 34 <option value="MACS">MACS</option>
35 <option selected="true" value="BED">BED</option> 35 <option selected="true" value="BED">BED</option>
36 </param> 36 </param>
37 37
38 <param name="detail" checked="true" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" /> 38 <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="" />
39 <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 <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="" />
40 </inputs> 40 </inputs>
41 <outputs> 41 <outputs>
42 <data format="txt" hidden="false" name="default"/> 42 <data format="txt" hidden="false" name="default"/>
43 </outputs> 43 </outputs>