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comparison bcftools_cnv.xml @ 2:cd84903d45c1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author iuc
date Mon, 03 Oct 2016 12:21:20 -0400
parents 2771c1ba81b1
children 801a440c28cc
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1:ef99a1afcb66 2:cd84903d45c1
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
3 <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description> 3 <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">cnv</token> 5 <token name="@EXECUTABLE@">cnv</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
97 <expand macro="macro_AF_file" /> 97 <expand macro="macro_AF_file" />
98 <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" /> 98 <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" />
99 </section> 99 </section>
100 <section name="sec_hmm" expanded="false" title="HMM Options"> 100 <section name="sec_hmm" expanded="false" title="HMM Options">
101 <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" /> 101 <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
102 <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" > 102 <param name="optimize" type="float" value="" min="0." max="1." label="Optimize" optional="True" >
103 <help> 103 <help>
104 Iteratively estimate the fraction of aberrant cells, down to the given fraction. 104 Iteratively estimate the fraction of aberrant cells, down to the given fraction.
105 Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise. 105 Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
106 </help> 106 </help>
107 </param> 107 </param>
109 <help> 109 <help>
110 The prior probability of the query and the control sample being the same. 110 The prior probability of the query and the control sample being the same.
111 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. 111 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
112 </help> 112 </help>
113 </param> 113 </param>
114 <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True"> 114 <param name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9" optional="True">
115 <help> 115 <help>
116 The HMM probability of transition to another copy number state. 116 The HMM probability of transition to another copy number state.
117 Increasing this value leads to smaller and more frequent calls. 117 Increasing this value leads to smaller and more frequent calls.
118 </help> 118 </help>
119 </param> 119 </param>
127 <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true" 127 <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true"
128 help="Expected BAF deviation in query, defaults to: 0.04" /> 128 help="Expected BAF deviation in query, defaults to: 0.04" />
129 <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" 129 <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true"
130 help="Expected BAF deviation in control, defaults to: 0.04" /> 130 help="Expected BAF deviation in control, defaults to: 0.04" />
131 131
132 <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" > 132 <param name="LRR_weight" type="float" label="LRR Weight" optional="True" >
133 <help> 133 <help>
134 Relative contribution from LRR. 134 Relative contribution from LRR.
135 With noisy data, this option can have big effect on the number of calls produced. 135 With noisy data, this option can have big effect on the number of calls produced.
136 In truly random noise (such as in simulated data), the value should be set high (1.0), i 136 In truly random noise (such as in simulated data), the value should be set high (1.0), i
137 but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2). 137 but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).
139 </param> 139 </param>
140 <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation" 140 <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation"
141 help="Expected LRR deviation in query, default is: 0.2" /> 141 help="Expected LRR deviation in query, default is: 0.2" />
142 <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" 142 <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation"
143 help="Expected LRR deviation in control, default is: 0.2" /> 143 help="Expected LRR deviation in control, default is: 0.2" />
144 <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True" 144 <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" value="10" optional="True"
145 help="Window of LRR moving average smoothing" /> 145 help="Window of LRR moving average smoothing" />
146 146
147 </section> 147 </section>
148 </inputs> 148 </inputs>
149 <outputs> 149 <outputs>