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comparison bamCorrelate.xml @ 5:c54d31467be4 draft

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Uploaded
author bgruening
date Fri, 29 Nov 2013 08:59:04 -0500
parents 9441b4e5d2d6
children 135f3bae5c56
comparison
equal deleted inserted replaced
4:ac935c35437a 5:c54d31467be4
13 13
14 @multiple_input_bams@ 14 @multiple_input_bams@
15 15
16 bamCorrelate 16 bamCorrelate
17 17
18 #if $mode.modeOpt == "bins": 18 $mode.modeOpt
19 bins
20 --binSize '$mode.binSize'
21 --numberOfSamples '$mode.numberOfSamples'
22 #else:
23 BED-file
24 --BED $mode.region_file
25 #end if
26 19
27 @THREADS@ 20 @THREADS@
28 21
29 --bamfiles #echo " ".join($files) 22 --bamfiles #echo " ".join($files)
30 --labels #echo " ".join($labels) 23 --labels #echo " ".join($labels)
36 --plotFile $newoutFileName 29 --plotFile $newoutFileName
37 30
38 #if $outputOpt.showOutputOpt == "yes" 31 #if $outputOpt.showOutputOpt == "yes"
39 --outRawCounts '$outFileRawCounts' 32 --outRawCounts '$outFileRawCounts'
40 --outFileCorMatrix '$outFileCorMatrix' 33 --outFileCorMatrix '$outFileCorMatrix'
34 #end if
35
36 #if $mode.modeOpt == "bins":
37 --binSize '$mode.binSize'
38 --numberOfSamples '$mode.numberOfSamples'
39 #else:
40 --BED $mode.region_file
41 #end if 41 #end if
42 42
43 ## options available in both modes 43 ## options available in both modes
44 #if $mode.advancedOpt.showAdvancedOpt == "yes": 44 #if $mode.advancedOpt.showAdvancedOpt == "yes":
45 45