Mercurial > repos > bgruening > deeptools
comparison bamCorrelate.xml @ 5:c54d31467be4 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 08:59:04 -0500 |
| parents | 9441b4e5d2d6 |
| children | 135f3bae5c56 |
comparison
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| 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 |