Mercurial > repos > bgruening > deeptools
comparison bamFingerprint.xml @ 40:20f8dafb554f draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 03 Feb 2014 12:38:00 -0500 |
| parents | 2f7edf06a5da |
| children | c5787c91cab8 |
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| 39:62786277147a | 40:20f8dafb554f |
|---|---|
| 28 #end if | 28 #end if |
| 29 #else | 29 #else |
| 30 --plotFileFormat 'png' | 30 --plotFileFormat 'png' |
| 31 #end if | 31 #end if |
| 32 | 32 |
| 33 #if str(region).strip() != '': | |
| 34 --region 'region' | |
| 35 #end if | |
| 36 | |
| 33 #if $advancedOpt.showAdvancedOpt == "yes": | 37 #if $advancedOpt.showAdvancedOpt == "yes": |
| 34 | |
| 35 #if str($advancedOpt.region.value) != '': | |
| 36 --region '$advancedOpt.region' | |
| 37 #end if | |
| 38 | |
| 39 --binSize '$advancedOpt.binSize' | 38 --binSize '$advancedOpt.binSize' |
| 40 --numberOfSamples '$advancedOpt.numberOfSamples' | 39 --numberOfSamples '$advancedOpt.numberOfSamples' |
| 41 | 40 |
| 42 $advancedOpt.doNotExtendPairedEnds | 41 $advancedOpt.doNotExtendPairedEnds |
| 43 $advancedOpt.ignoreDuplicates | 42 $advancedOpt.ignoreDuplicates |
| 52 </command> | 51 </command> |
| 53 | 52 |
| 54 <inputs> | 53 <inputs> |
| 55 <expand macro="multiple_input_bams" /> | 54 <expand macro="multiple_input_bams" /> |
| 56 | 55 |
| 56 | |
| 57 <param name="fragmentLength" type="integer" value="200" min="1" | 57 <param name="fragmentLength" type="integer" value="200" min="1" |
| 58 label="Length of the average fragment size"/> | 58 label="Length of the average fragment size"/> |
| 59 | |
| 60 <expand macro="region_limit_operation" /> | |
| 61 | |
| 59 <conditional name="advancedOpt"> | 62 <conditional name="advancedOpt"> |
| 60 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | 63 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
| 61 <option value="no" selected="true">no</option> | 64 <option value="no" selected="true">no</option> |
| 62 <option value="yes">yes</option> | 65 <option value="yes">yes</option> |
| 63 </param> | 66 </param> |
| 64 <when value="no" /> | 67 <when value="no" /> |
| 65 <when value="yes"> | 68 <when value="yes"> |
| 66 <param name="region" type="text" value="" | |
| 67 label="Region of the genome to limit the operation to" | |
| 68 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> | |
| 69 | |
| 70 <param name="binSize" type="integer" value="10000" min="1" | 69 <param name="binSize" type="integer" value="10000" min="1" |
| 71 label="Bin size in bp" | 70 label="Bin size in bp" |
| 72 help="Length in base pairs for a window used to sample the genome."/> | 71 help="Length in base pairs for a window used to sample the genome."/> |
| 73 | 72 |
| 74 <param name="numberOfSamples" type="integer" value="100000" min="1" | 73 <param name="numberOfSamples" type="integer" value="100000" min="1" |