Mercurial > repos > alenail > chipsequtil
comparison chipsequtil/map_to_known_genes.xml @ 8:a30aa2806375 draft
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author | alenail |
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date | Mon, 04 Apr 2016 15:02:03 -0400 |
parents | 124231ed2402 |
children | a92644537c7d |
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7:007d99e2ae91 | 8:a30aa2806375 |
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21 </command> | 21 </command> |
22 <inputs> | 22 <inputs> |
23 <param name="knownGeneFile" type="data" label="knownGene file" help="" optional="false" /> | 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" /> | 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" /> | 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 | 26 |
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" /> | 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" /> |
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" /> | 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" /> |
30 | 29 |
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="" /> | 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="" /> |
37 | 36 |
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="" /> | 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="" /> |
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="" /> | 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="" /> |
40 </inputs> | 39 </inputs> |
41 <outputs> | 40 <outputs> |
42 <data format="txt" hidden="false" name="default"/> | 41 <data format="txt" hidden="false" name="peaksOutput"/> |
43 </outputs> | 42 </outputs> |
44 <help></help> | 43 <help></help> |
45 </tool> | 44 </tool> |