Mercurial > repos > alenail > chipsequtil
comparison chipsequtil/map_to_known_genes.xml @ 6:124231ed2402 draft
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author | alenail |
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date | Mon, 04 Apr 2016 14:56:51 -0400 |
parents | 0eaa8225a09a |
children | a30aa2806375 |
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5:199989365def | 6:124231ed2402 |
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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> |