Mercurial > repos > bgruening > deeptools

comparison bamCompare.xml @ 17:ef65d6b68ccc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
36 #if $comparison.normalization.type=='rpkm': 36 #if $comparison.normalization.type=='rpkm':
37 --normalizeUsingRPKM 37 --normalizeUsingRPKM
38 #elif $comparison.normalization.type=='1x': 38 #elif $comparison.normalization.type=='1x':
39 --normalizeTo1x $comparison.normalization.normalizeTo1x 39 --normalizeTo1x $comparison.normalization.normalizeTo1x
40 #end if 40 #end if
41
42 #if str($comparison.ignoreForNormalization).strip() != '':
43 --ignoreForNormalization $comparison.ignoreForNormalization
44 #end if
45
46 #end if 41 #end if
47 42
48 #if $advancedOpt.showAdvancedOpt == "yes": 43 #if $advancedOpt.showAdvancedOpt == "yes":
49 #if $advancedOpt.smoothLength: 44 #if $advancedOpt.smoothLength:
50 --smoothLength '$advancedOpt.smoothLength' 45 --smoothLength '$advancedOpt.smoothLength'
51 #end if 46 #end if
52 47
53 #if str($advancedOpt.region.value) != '': 48 #if str($advancedOpt.region.value) != '':
54 --region '$advancedOpt.region' 49 --region '$advancedOpt.region'
55 #end if 50 #end if
56 51
57 $advancedOpt.doNotExtendPairedEnds 52 $advancedOpt.doNotExtendPairedEnds
58 $advancedOpt.ignoreDuplicates 53 $advancedOpt.ignoreDuplicates
59 54
60 #if $advancedOpt.minMappingQuality: 55 #if $advancedOpt.minMappingQuality:
61 --minMappingQuality '$advancedOpt.minMappingQuality' 56 --minMappingQuality '$advancedOpt.minMappingQuality'
62 #end if 57 #end if
63 58
64 --missingDataAsZero $advancedOpt.missingDataAsZero 59 --missingDataAsZero $advancedOpt.missingDataAsZero
60
61 #if str($advancedOpt.ignoreForNormalization).strip() != '':
62 --ignoreForNormalization $advancedOpt.ignoreForNormalization
63 #end if
65 64
66 #end if 65 #end if
67 66
68 </command> 67 </command>
69 68
126 <param name="normalizeTo1x" type="integer" value="2150570000" 125 <param name="normalizeTo1x" type="integer" value="2150570000"
127 label="Report normalized coverage to 1x sequenceing depth" 126 label="Report normalized coverage to 1x sequenceing depth"
128 help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/> 127 help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
129 </when> 128 </when>
130 </conditional> 129 </conditional>
131 <param name="ignoreForNormalization" type="text" value="" size="50"
132 label="regions that should be excluded for calculating the scaling factor"
133 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" />
134 </when> 130 </when>
135 </conditional> 131 </conditional>
136 132
137 <param name="outFileFormat" type="select" label="Coverage file format"> 133 <param name="outFileFormat" type="select" label="Coverage file format">
138 <option value="bigwig" selected="true">bigwig</option> 134 <option value="bigwig" selected="true">bigwig</option>
145 <option value="yes">yes</option> 141 <option value="yes">yes</option>
146 </param> 142 </param>
147 <when value="no" /> 143 <when value="no" />
148 <when value="yes"> 144 <when value="yes">
149 145
150 <param name="smoothLength" type="integer" value="1" optional="true" min="1" 146 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
151 label="Smooth values using the following length (in bp)" 147 label="Smooth values using the following length (in bp)"
152 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."/> 148 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."/>
153 149
154 <param name="region" type="text" value="" 150 <param name="region" type="text" value=""
155 label="Region of the genome to limit the operation to" 151 label="Region of the genome to limit the operation to"
156 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;" /> 152 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;" />
157 153
158 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 154 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
159 label="Do not extend paired ends" 155 label="Do not extend paired ends"
160 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."/> 156 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."/>
161 157
162 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" 158 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
163 label="Ignore duplicates" 159 label="Ignore duplicates"
164 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." /> 160 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." />
165 161
166 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" 162 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
167 label="Minimum mapping quality (e.g. BOWTIE2 measures)" 163 label="Minimum mapping quality (e.g. BOWTIE2 measures)"
168 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."/> 164 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."/>
169 165
170 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" 166 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
171 label ="Treat missing data as zero" 167 label ="Treat missing data as zero"
172 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." /> 168 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
169
170 <param name="ignoreForNormalization" type="text" value="" size="50"
171 label="regions that should be excluded for calculating the scaling factor"
172 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" />
173
173 </when> 174 </when>
174 </conditional> 175 </conditional>
175 176
176 </inputs> 177 </inputs>
177 <outputs> 178 <outputs>