comparison hicDetectLoops.xml @ 2:cabc992c6207 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 38accbb2df53ff03e810a3b92f4723fa29636950"

1:2d1988b74bf6

<tool id="hicexplorer_hicdetectloops" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>searches for enriched regions</description>
    <macros>
        <token name="@BINARY@">hicDetectLoops</token>
        <import>macros.xml</import>
    </macros>

                                This does NOT influence the p-value for the neighborhood testing." value='0.05'/>
        <param argument="--peakInteractionsThreshold" type="integer" label="Minimum interaction number" help= "The minimum number of interactions a detected peaks needs to have to be considered." value='5' />
        <param argument="--maximumInteractionPercentageThreshold" type="float" value='0.1' label="Maximum interaction share" help= "For each genomic distance the maximum value is considered and all candidates need to have at least \'max_value * maximumInteractionPercentageThreshold\' interactions." />
        <param argument="--pValue" type="float" label="P-value" help= "Rejection level for the statistical test for H0. H0 is peak region and background have the same distribution." value='0.05'/>
        <param argument="--maxLoopDistance" optional='true'  type="integer" label="Maximal loop distance" help= "Maximum genomic distance of a loop, usually loops are within a distance of ~2MB." value='2000000'/>
        <param argument="--minLoopDistance" optional='true'  type="integer" label="Maximal loop distance" help= "Minimum genomic distance of a loop to be considered." value='100000'/>
        <param argument="--chromosomes" optional='true'  type="text" label="Chromosomes to include" help= "Chromosomes to include in the analysis. If not set, all chromosomes are included." />
        <param argument="--region" optional='true'  type="text" label="Chromosomes to include" help= "The format is chr:start-end." />
        <param name="statisticalTest_selector" type="select" label="Stistical test">
            <option value="wilcoxon-rank-sum" selected="True">Wilcoxon rank-sum'</option>
            <option value="anderson-darling">Anderson-Darling</option>

2:cabc992c6207

<tool id="hicexplorer_hicdetectloops" name="@BINARY@" version="@WRAPPER_VERSION@.1">
    <description>searches for enriched regions</description>
    <macros>
        <token name="@BINARY@">hicDetectLoops</token>
        <import>macros.xml</import>
    </macros>

                                This does NOT influence the p-value for the neighborhood testing." value='0.05'/>
        <param argument="--peakInteractionsThreshold" type="integer" label="Minimum interaction number" help= "The minimum number of interactions a detected peaks needs to have to be considered." value='5' />
        <param argument="--maximumInteractionPercentageThreshold" type="float" value='0.1' label="Maximum interaction share" help= "For each genomic distance the maximum value is considered and all candidates need to have at least \'max_value * maximumInteractionPercentageThreshold\' interactions." />
        <param argument="--pValue" type="float" label="P-value" help= "Rejection level for the statistical test for H0. H0 is peak region and background have the same distribution." value='0.05'/>
        <param argument="--maxLoopDistance" optional='true'  type="integer" label="Maximal loop distance" help= "Maximum genomic distance of a loop, usually loops are within a distance of ~2MB." value='2000000'/>
        <param argument="--minLoopDistance" optional='true'  type="integer" label="Minimum loop distance" help= "Minimum genomic distance of a loop to be considered." value='100000'/>
        <param argument="--chromosomes" optional='true'  type="text" label="Chromosomes to include" help= "Chromosomes to include in the analysis. If not set, all chromosomes are included." />
        <param argument="--region" optional='true'  type="text" label="Chromosomes to include" help= "The format is chr:start-end." />
        <param name="statisticalTest_selector" type="select" label="Stistical test">
            <option value="wilcoxon-rank-sum" selected="True">Wilcoxon rank-sum'</option>
            <option value="anderson-darling">Anderson-Darling</option>