comparison bcftools_cnv.xml @ 2:cd84903d45c1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6

1:ef99a1afcb66

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
    <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
    <macros>
        <token name="@EXECUTABLE@">cnv</token>
        <import>macros.xml</import>
    </macros>

            <expand macro="macro_AF_file" />
            <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" />
        </section>
        <section name="sec_hmm" expanded="false" title="HMM Options">
            <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
            <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" >
                <help>
                  Iteratively estimate the fraction of aberrant cells, down to the given fraction. 
                  Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
                </help>
            </param>

                <help>
                    The prior probability of the query and the control sample being the same. 
                    Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
                </help>
            </param>
            <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True">
                <help>
                    The HMM probability of transition to another copy number state. 
                    Increasing this value leads to smaller and more frequent calls. 
                </help>
            </param>

            <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true" 
                   help="Expected BAF deviation in query, defaults to: 0.04" />
            <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" 
                   help="Expected BAF deviation in control, defaults to: 0.04" />

            <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" >
                <help>
                    Relative contribution from LRR.  
                    With noisy data, this option can have big effect on the number of calls produced. 
                    In truly random noise (such as in simulated data), the value should be set high (1.0), i
                    but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).

            </param>
            <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation" 
                   help="Expected LRR deviation in query, default is: 0.2" />
            <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" 
                   help="Expected LRR deviation in control, default is: 0.2" />
            <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True" 
                   help="Window of LRR moving average smoothing" />

        </section>
    </inputs>
    <outputs>

2:cd84903d45c1

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
    <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
    <macros>
        <token name="@EXECUTABLE@">cnv</token>
        <import>macros.xml</import>
    </macros>

            <expand macro="macro_AF_file" />
            <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" />
        </section>
        <section name="sec_hmm" expanded="false" title="HMM Options">
            <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
            <param name="optimize" type="float" value="" min="0." max="1." label="Optimize" optional="True" >
                <help>
                  Iteratively estimate the fraction of aberrant cells, down to the given fraction. 
                  Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
                </help>
            </param>

                <help>
                    The prior probability of the query and the control sample being the same. 
                    Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
                </help>
            </param>
            <param name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9" optional="True">
                <help>
                    The HMM probability of transition to another copy number state. 
                    Increasing this value leads to smaller and more frequent calls. 
                </help>
            </param>

            <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true" 
                   help="Expected BAF deviation in query, defaults to: 0.04" />
            <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" 
                   help="Expected BAF deviation in control, defaults to: 0.04" />

            <param name="LRR_weight" type="float" label="LRR Weight" optional="True" >
                <help>
                    Relative contribution from LRR.  
                    With noisy data, this option can have big effect on the number of calls produced. 
                    In truly random noise (such as in simulated data), the value should be set high (1.0), i
                    but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).

            </param>
            <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation" 
                   help="Expected LRR deviation in query, default is: 0.2" />
            <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" 
                   help="Expected LRR deviation in control, default is: 0.2" />
            <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" value="10" optional="True" 
                   help="Window of LRR moving average smoothing" />

        </section>
    </inputs>
    <outputs>