Mercurial > repos > bgruening > deeptools

comparison bamCorrelate.xml @ 3:9441b4e5d2d6 draft

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Uploaded
author bgruening
date Sat, 16 Nov 2013 07:50:32 -0500
parents a22ccc261bb3
children c54d31467be4
comparison
equal deleted inserted replaced
2:b5da81864541 3:9441b4e5d2d6
13 13
14 @multiple_input_bams@ 14 @multiple_input_bams@
15 15
16 bamCorrelate 16 bamCorrelate
17 17
18 #if $mode.modeOpt == "bins":
19 bins
20 --binSize '$mode.binSize'
21 --numberOfSamples '$mode.numberOfSamples'
22 #else:
23 BED-file
24 --BED $mode.region_file
25 #end if
26
18 @THREADS@ 27 @THREADS@
19 28
20 --bamfiles #echo " ".join($files) 29 --bamfiles #echo " ".join($files)
21 --labels #echo " ".join($labels) 30 --labels #echo " ".join($labels)
22 31
27 --plotFile $newoutFileName 36 --plotFile $newoutFileName
28 37
29 #if $outputOpt.showOutputOpt == "yes" 38 #if $outputOpt.showOutputOpt == "yes"
30 --outRawCounts '$outFileRawCounts' 39 --outRawCounts '$outFileRawCounts'
31 --outFileCorMatrix '$outFileCorMatrix' 40 --outFileCorMatrix '$outFileCorMatrix'
32 #end if
33
34 #if $mode.modeOpt == "bins":
35 --binSize '$mode.binSize'
36 --numberOfSamples '$mode.numberOfSamples'
37 #else:
38 --BED $mode.region_file
39 #end if 41 #end if
40 42
41 ## options available in both modes 43 ## options available in both modes
42 #if $mode.advancedOpt.showAdvancedOpt == "yes": 44 #if $mode.advancedOpt.showAdvancedOpt == "yes":
43 45