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comparison bamCoverage.xml @ 29:3a2aab18a217 draft

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Uploaded
author bgruening
date Tue, 16 Sep 2014 13:46:05 -0400
parents f7712a057440
children 5231f398d784
comparison
equal deleted inserted replaced
28:f7712a057440 29:3a2aab18a217
44 $advancedOpt.ignoreDuplicates 44 $advancedOpt.ignoreDuplicates
45 45
46 #if $advancedOpt.minMappingQuality: 46 #if $advancedOpt.minMappingQuality:
47 --minMappingQuality '$advancedOpt.minMappingQuality' 47 --minMappingQuality '$advancedOpt.minMappingQuality'
48 #end if 48 #end if
49
50 --missingDataAsZero $advancedOpt.missingDataAsZero
49 51
50 ##if str($advancedOpt.ignoreForNormalization).strip() != '': 52 ##if str($advancedOpt.ignoreForNormalization).strip() != '':
51 ## --ignoreForNormalization $advancedOpt.ignoreForNormalization 53 ## --ignoreForNormalization $advancedOpt.ignoreForNormalization
52 ##end if 54 ##end if
53 55
112 114
113 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" 115 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
114 label="Minimum mapping quality" 116 label="Minimum mapping quality"
115 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> 117 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
116 118
119 <expand macro="missingDataAsZero" />
120
117 <!-- <param name="ignoreForNormalization" type="text" value="" size="50" 121 <!-- <param name="ignoreForNormalization" type="text" value="" size="50"
118 label="regions that should be excluded for calculating the scaling factor" 122 label="regions that should be excluded for calculating the scaling factor"
119 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" /> 123 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
120 --> 124 -->
121 </when> 125 </when>
156 ----- 160 -----
157 161
158 @REFERENCES@ 162 @REFERENCES@
159 163
160 </help> 164 </help>
165 <expand macro="citations" />
161 </tool> 166 </tool>