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comparison bamCoverage.xml @ 17:ef65d6b68ccc draft

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Uploaded
author bgruening
date Sat, 21 Dec 2013 14:26:06 -0500
parents 135f3bae5c56
children 5ea8782d650c
comparison
equal deleted inserted replaced
16:16310f8b24d5 17:ef65d6b68ccc
24 --normalizeTo1x $scaling.normalizeTo1x 24 --normalizeTo1x $scaling.normalizeTo1x
25 #elif $scaling.type=='own': 25 #elif $scaling.type=='own':
26 --scaleFactor $scaling.scaleFactor 26 --scaleFactor $scaling.scaleFactor
27 #end if 27 #end if
28 28
29 ##if str($ignoreForNormalization).strip() != '':
30 ## --ignoreForNormalization $ignoreForNormalization
31 ##end if
32
33 #if $advancedOpt.showAdvancedOpt == "yes": 29 #if $advancedOpt.showAdvancedOpt == "yes":
34 #if $advancedOpt.smoothLength: 30 #if $advancedOpt.smoothLength:
35 --smoothLength '$advancedOpt.smoothLength' 31 --smoothLength '$advancedOpt.smoothLength'
36 #end if 32 #end if
37 33
42 $advancedOpt.ignoreDuplicates 38 $advancedOpt.ignoreDuplicates
43 39
44 #if $advancedOpt.minMappingQuality: 40 #if $advancedOpt.minMappingQuality:
45 --minMappingQuality '$advancedOpt.minMappingQuality' 41 --minMappingQuality '$advancedOpt.minMappingQuality'
46 #end if 42 #end if
43
44 ##if str($advancedOpt.ignoreForNormalization).strip() != '':
45 ## --ignoreForNormalization $advancedOpt.ignoreForNormalization
46 ##end if
47 47
48 #end if 48 #end if
49 </command> 49 </command>
50 50
51 <inputs> 51 <inputs>
78 <param name="scaleFactor" type="float" value="1" size="3" 78 <param name="scaleFactor" type="float" value="1" size="3"
79 label="Scale factor to multiply all values" /> 79 label="Scale factor to multiply all values" />
80 </when> 80 </when>
81 </conditional> 81 </conditional>
82 82
83 <!--
84 Not yet supported.
85 <param name="ignoreForNormalization" type="text" value="" size="50"
86 label="regions that should be excluded for calculating the scaling factor"
87 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" />
88 -->
89
90 <param name="outFileFormat" type="select" label="Coverage file format"> 83 <param name="outFileFormat" type="select" label="Coverage file format">
91 <option value="bigwig" selected="true">bigwig</option> 84 <option value="bigwig" selected="true">bigwig</option>
92 <option value="bedgraph">bedgraph</option> 85 <option value="bedgraph">bedgraph</option>
93 </param> 86 </param>
94 87
116 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 109 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
117 110
118 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" 111 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
119 label="Minimum mapping quality" 112 label="Minimum mapping quality"
120 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."/> 113 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."/>
114
115 <!-- <param name="ignoreForNormalization" type="text" value="" size="50"
116 label="regions that should be excluded for calculating the scaling factor"
117 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" />
118 -->
121 </when> 119 </when>
122 </conditional> 120 </conditional>
123 </inputs> 121 </inputs>
124 <outputs> 122 <outputs>
125 <data format="bigwig" name="outFileName"> 123 <data format="bigwig" name="outFileName">