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comparison bamCompare.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
43 #else: 43 #else:
44 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt 44 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
45 #end if 45 #end if
46 46
47 #end if 47 #end if
48 #elif $comparison.type in ['ratio','log2']:
49 --pseudocount $comparison.pseudocount
48 #end if 50 #end if
49 51
50 #if str($region).strip() != '': 52 #if str($region).strip() != '':
51 --region '$region' 53 --region '$region'
52 #end if 54 #end if
115 label="How to compare the two files"> 117 label="How to compare the two files">
116 <option value="log2" selected="true">compute log2 of the number of reads ratio</option> 118 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
117 <option value="ratio">compute the ratio of the number of reads</option> 119 <option value="ratio">compute the ratio of the number of reads</option>
118 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option> 120 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
119 </param> 121 </param>
120 <when value="log2" /> 122 <when value="log2">
121 <when value="ratio" /> 123 <expand macro="pseudocount" />
124 </when>
125 <when value="ratio">
126 <expand macro="pseudocount" />
127 </when>
122 <when value="subtract"> 128 <when value="subtract">
123 <conditional name="normalization"> 129 <conditional name="normalization">
124 <param name="type" type="select" label="Normalization method" > 130 <param name="type" type="select" label="Normalization method" >
125 <option value="1x">Normalize coverage to 1x</option> 131 <option value="1x">Normalize coverage to 1x</option>
126 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option> 132 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
164 170
165 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" 171 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
166 label="Minimum mapping quality (e.g. BOWTIE2 measures)" 172 label="Minimum mapping quality (e.g. BOWTIE2 measures)"
167 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."/> 173 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."/>
168 174
169 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" 175 <expand macro="missingDataAsZero" />
170 label ="Treat missing data as zero"
171 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." />
172 176
173 <param name="ignoreForNormalization" type="text" value="" size="50" 177 <param name="ignoreForNormalization" type="text" value="" size="50"
174 label="regions that should be excluded for calculating the scaling factor" 178 label="regions that should be excluded for calculating the scaling factor"
175 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" /> 179 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" />
176 180
220 ----- 224 -----
221 225
222 @REFERENCES@ 226 @REFERENCES@
223 227
224 </help> 228 </help>
229 <expand macro="citations" />
225 </tool> 230 </tool>