Mercurial > repos > pavlo-lutsik > rnbeads

comparison automated.settings.xml.txt @ 13:d6cdc73fd57e draft

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author pavlo-lutsik
date Sun, 21 Apr 2013 18:04:11 -0400
parents ce411254e4a9
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12:73e7d00a9a19 13:d6cdc73fd57e
1 <param name="analysisName" type="text" label="analysis.name, character" value=""/>
2 <param name="logging" type="select" label="logging, logical" value="1">
3 <option value="True">True</option>
4 <option value="False">False</option>
5 </param>
6 <param name="email" type="text" label="email, character" value=""/>
7 <param name="assembly" type="text" label="assembly, character" value="hg19"/>
8 <param name="analyzeSites" type="select" label="analyze.sites, logical" value="1">
9 <option value="True">True</option>
10 <option value="False">False</option>
11 </param>
12 <param name="regionTypes" type="text" label="region.types, character vector" value="tiling,genes,promoters,cpgislands"/>
13 <param name="identifiersColumn" type="text" label="identifiers.column, character" value=""/>
14 <param name="pointsCategory" type="text" label="points.category, integer vector" value="16,17,3,15,4,7,8"/>
15 <param name="colorsCategory" type="text" label="colors.category, character vector" value="#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666"/>
16 <param name="colorsGradient" type="text" label="colors.gradient, character vector" value="#132B43,#56B1F7"/>
17 <param name="minGroupSize" type="text" label="min.group.size, integer" value="2"/>
18 <param name="maxGroupCount" type="text" label="max.group.count, integer" value="8"/>
19 <param name="gzLargeFiles" type="select" label="gz.large.files, logical" value="0">
20 <option value="True">True</option>
21 <option value="False">False</option>
22 </param>
23 <param name="strandSpecific" type="select" label="strand.specific, logical" value="0">
24 <option value="True">True</option>
25 <option value="False">False</option>
26 </param>
27 <param name="replicateIdColumn" type="text" label="replicate.id.column, character" value=""/>
28 <param name="loadingNormalization" type="select" label="loading.normalization, logical" value="1">
29 <option value="True">True</option>
30 <option value="False">False</option>
31 </param>
32 <param name="loadingDefaultDataType" type="text" label="loading.default.data.type, character" value="idat.dir"/>
33 <param name="loadingTableSeparator" type="text" label="loading.table.separator, character" value=" "/>
34 <param name="loadingBedStyle" type="text" label="loading.bed.style, character" value="BisSNP"/>
35 <param name="loadingBedColumns" type="text" label="loading.bed.columns, integer vector" value="1,2,3,6,4,5"/>
36 <param name="loadingBedFrameShift" type="text" label="loading.bed.frame.shift, integer" value="1"/>
37 <param name="normalizationMethod" type="text" label="normalization.method, character" value="illumina"/>
38 <param name="normalizationSubtractBackground" type="select" label="normalization.subtract.background, logical" value="0">
39 <option value="True">True</option>
40 <option value="False">False</option>
41 </param>
42 <param name="qc" type="select" label="qc, logical" value="1">
43 <option value="True">True</option>
44 <option value="False">False</option>
45 </param>
46 <param name="qcBoxplots" type="select" label="qc.boxplots, logical" value="1">
47 <option value="True">True</option>
48 <option value="False">False</option>
49 </param>
50 <param name="qcBarplots" type="select" label="qc.barplots, logical" value="1">
51 <option value="True">True</option>
52 <option value="False">False</option>
53 </param>
54 <param name="qcNegativeBoxplot" type="select" label="qc.negative.boxplot, logical" value="1">
55 <option value="True">True</option>
56 <option value="False">False</option>
57 </param>
58 <param name="qcSnpHeatmap" type="select" label="qc.snp.heatmap, logical" value="1">
59 <option value="True">True</option>
60 <option value="False">False</option>
61 </param>
62 <param name="qcSnpBoxplot" type="select" label="qc.snp.boxplot, logical" value="0">
63 <option value="True">True</option>
64 <option value="False">False</option>
65 </param>
66 <param name="qcSnpBarplot" type="select" label="qc.snp.barplot, logical" value="0">
67 <option value="True">True</option>
68 <option value="False">False</option>
69 </param>
70 <param name="qcSampleBatchSize" type="text" label="qc.sample.batch.size, integer" value="50"/>
71 <param name="filteringContextRemoval" type="text" label="filtering.context.removal, character vector" value="CC,CAG,CAH,CTG,CTH,Other"/>
72 <param name="filteringSnp" type="select" label="filtering.snp, logical" value="1">
73 <option value="True">True</option>
74 <option value="False">False</option>
75 </param>
76 <param name="filteringSnpFrequency" type="text" label="filtering.snp.frequency, double" value="0.01"/>
77 <param name="filteringSnpAccepted" type="text" label="filtering.snp.accepted, integer" value="2"/>
78 <param name="filteringSexChromosomesRemoval" type="select" label="filtering.sex.chromosomes.removal, logical" value="0">
79 <option value="True">True</option>
80 <option value="False">False</option>
81 </param>
82 <param name="filteringMissingValueQuantile" type="text" label="filtering.missing.value.quantile, double" value="1"/>
83 <param name="filteringCoverageThreshold" type="text" label="filtering.coverage.threshold, integer" value="5"/>
84 <param name="filteringLowCoverageMasking" type="select" label="filtering.low.coverage.masking, logical" value="0">
85 <option value="True">True</option>
86 <option value="False">False</option>
87 </param>
88 <param name="filteringHighCoverageOutliers" type="select" label="filtering.high.coverage.outliers, logical" value="0">
89 <option value="True">True</option>
90 <option value="False">False</option>
91 </param>
92 <param name="filteringGreedycut" type="select" label="filtering.greedycut, logical" value="1">
93 <option value="True">True</option>
94 <option value="False">False</option>
95 </param>
96 <param name="filteringGreedycutPvalueThreshold" type="text" label="filtering.greedycut.pvalue.threshold, double" value="0.05"/>
97 <param name="filteringGreedycutRcTies" type="text" label="filtering.greedycut.rc.ties, character" value="row"/>
98 <param name="filteringDeviationThreshold" type="text" label="filtering.deviation.threshold, double" value="0"/>
99 <param name="batch" type="select" label="batch, logical" value="1">
100 <option value="True">True</option>
101 <option value="False">False</option>
102 </param>
103 <param name="batchDreductionColumns" type="text" label="batch.dreduction.columns, integer vector" value=""/>
104 <param name="batchPrincipalComponents" type="text" label="batch.principal.components, integer" value="8"/>
105 <param name="batchCorrelationColumns" type="text" label="batch.correlation.columns, integer vector" value=""/>
106 <param name="batchCorrelationPvalueThreshold" type="text" label="batch.correlation.pvalue.threshold, double" value="0.01"/>
107 <param name="batchCorrelationPermutations" type="text" label="batch.correlation.permutations, integer" value="10000"/>
108 <param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">
109 <option value="True">True</option>
110 <option value="False">False</option>
111 </param>
112 <param name="profiles" type="select" label="profiles, logical" value="1">
113 <option value="True">True</option>
114 <option value="False">False</option>
115 </param>
116 <param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">
117 <option value="True">True</option>
118 <option value="False">False</option>
119 </param>
120 <param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">
121 <option value="True">True</option>
122 <option value="False">False</option>
123 </param>
124 <param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">
125 <option value="True">True</option>
126 <option value="False">False</option>
127 </param>
128 <param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>
129 <param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">
130 <option value="True">True</option>
131 <option value="False">False</option>
132 </param>
133 <param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>
134 <param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>
135 <param name="differential" type="select" label="differential, logical" value="1">
136 <option value="True">True</option>
137 <option value="False">False</option>
138 </param>
139 <param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>
140 <param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>
141 <param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">
142 <option value="True">True</option>
143 <option value="False">False</option>
144 </param>
145 <param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>
146 <param name="exportToBed" type="select" label="export.to.bed, logical" value="1">
147 <option value="True">True</option>
148 <option value="False">False</option>
149 </param>
150 <param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">
151 <option value="True">True</option>
152 <option value="False">False</option>
153 </param>
154 <param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>
155 <param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>
156 <param name="loggingMemory" type="select" label="logging.memory, logical" value="0">
157 <option value="True">True</option>
158 <option value="False">False</option>
159 </param>
160 <param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">
161 <option value="True">True</option>
162 <option value="False">False</option>
163 </param>