Mercurial > repos > bgruening > deeptools

comparison bamCompare.xml @ 40:20f8dafb554f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 03 Feb 2014 12:38:00 -0500
parents 2f7edf06a5da
children c5787c91cab8
comparison
equal deleted inserted replaced
39:62786277147a 40:20f8dafb554f
45 #end if 45 #end if
46 46
47 #end if 47 #end if
48 #end if 48 #end if
49 49
50 #if str(region).strip() != '':
51 --region 'region'
52 #end if
53
50 #if $advancedOpt.showAdvancedOpt == "yes": 54 #if $advancedOpt.showAdvancedOpt == "yes":
51 #if $advancedOpt.smoothLength: 55 #if $advancedOpt.smoothLength:
52 --smoothLength '$advancedOpt.smoothLength' 56 --smoothLength '$advancedOpt.smoothLength'
53 #end if
54
55 #if str($advancedOpt.region.value) != '':
56 --region '$advancedOpt.region'
57 #end if 57 #end if
58 58
59 $advancedOpt.doNotExtendPairedEnds 59 $advancedOpt.doNotExtendPairedEnds
60 $advancedOpt.ignoreDuplicates 60 $advancedOpt.ignoreDuplicates
61 61
138 <param name="outFileFormat" type="select" label="Coverage file format"> 138 <param name="outFileFormat" type="select" label="Coverage file format">
139 <option value="bigwig" selected="true">bigwig</option> 139 <option value="bigwig" selected="true">bigwig</option>
140 <option value="bedgraph">bedgraph</option> 140 <option value="bedgraph">bedgraph</option>
141 </param> 141 </param>
142 142
143 <expand macro="region_limit_operation" />
144
143 <conditional name="advancedOpt"> 145 <conditional name="advancedOpt">
144 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 146 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
145 <option value="no" selected="true">no</option> 147 <option value="no" selected="true">no</option>
146 <option value="yes">yes</option> 148 <option value="yes">yes</option>
147 </param> 149 </param>
149 <when value="yes"> 151 <when value="yes">
150 152
151 <param name="smoothLength" type="integer" value="1" optional="true" min="1" 153 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
152 label="Smooth values using the following length (in bp)" 154 label="Smooth values using the following length (in bp)"
153 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> 155 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
154
155 <param name="region" type="text" value=""
156 label="Region of the genome to limit the operation to"
157 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
158 156
159 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 157 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
160 label="Do not extend paired ends" 158 label="Do not extend paired ends"
161 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> 159 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
162 160