Mercurial > repos > bgruening > hicexplorer_chicviewpoint

comparison chicViewpoint.xml @ 3:8fb584526458 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 14:32:20 -0400
parents 0dabfd9a496b
children 78b70d78a596
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2:0dabfd9a496b 3:8fb584526458
20 --matrices $m 20 --matrices $m
21 --range $rangeUpstream $rangeDownstream 21 --range $rangeUpstream $rangeDownstream
22 --referencePoints '$referencePoints' 22 --referencePoints '$referencePoints'
23 --averageContactBin $averageContactBin 23 --averageContactBin $averageContactBin
24 --fixateRange $fixateRange 24 --fixateRange $fixateRange
25 --decimalPlaces $decimalPlaces
25 --threads @THREADS@ 26 --threads @THREADS@
26 --backgroundModelFile '$backgroundModelFile' 27 --backgroundModelFile '$backgroundModelFile'
27 --outputFolder interactionFiles 28 --outputFolder interactionFiles
28 $writeFileNamesToFile 29 $writeFileNamesToFile
29 30
40 <param argument="--backgroundModelFile" type="data" format='tabular' 41 <param argument="--backgroundModelFile" type="data" format='tabular'
41 label="Background model" 42 label="Background model"
42 help="The background file computed by chicViewpointBackgroundModel" /> 43 help="The background file computed by chicViewpointBackgroundModel" />
43 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/> 44 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
44 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/> 45 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
46 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.'/>
47
45 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" 48 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)"
46 help="Set this parameter if you want to use the batch processing mode for the further analysis."/> 49 help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
47 </inputs> 50 </inputs>
48 <outputs> 51 <outputs>
49 <collection name="interactionFilesCollection" type="list" label="Interaction files"> 52 <collection name="interactionFilesCollection" type="list" label="Interaction files">