comparison hicDetectLoops.xml @ 8:0410b6aada45 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

7:0d6c2ff54c76

            --threads @THREADS@ -tpc @THREADS@
]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param argument="--peakWidth" type="integer" optional='true' label="Peak width" help= "The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins." />
        <param argument="--windowSize" type="integer" optional='true' label="Window size" help= "The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak
                           region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" />
        <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates.
                                For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given.
                                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' />

        <!-- new-->
        <param argument="--obsExpThreshold" type="float" label="Obs/exp interaction threshold" help= "The minimum number of obs/exp interactions a detected peaks needs to have to be considered" value='1.5' />

        <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="--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 argument="--expected" type="select" label="Method to compute the expected value">
            <option value="mean" selected="True">mean</option>
            <option value="mean_nonzero">mean_nonzero</option>
            <option value="mean_nonzero_ligation">mean_nonzero_ligation</option>
        </param>
    </inputs>
    <outputs>
        <data name='output_loops' from_work_dir='output_loop.bedgraph' format='bedgraph' label='Computed loops' />
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
            <param name="maxLoopDistance" value="30000000" />

8:0410b6aada45

            --threads @THREADS@ -tpc @THREADS@
]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param argument="--peakWidth" type="integer" optional="true" label="Peak width" help= "The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins." />
        <param argument="--windowSize" type="integer" optional="true" label="Window size" help= "The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak
                           region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" />
        <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates.
                                For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given.
                                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" />

        <!-- new-->
        <param argument="--obsExpThreshold" type="float" label="Obs/exp interaction threshold" help= "The minimum number of obs/exp interactions a detected peaks needs to have to be considered" value="1.5" />

        <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="--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 argument="--expected" type="select" label="Method to compute the expected value">
            <option value="mean" selected="True">mean</option>
            <option value="mean_nonzero">mean_nonzero</option>
            <option value="mean_nonzero_ligation">mean_nonzero_ligation</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_loops" from_work_dir="output_loop.bedgraph" format="bedgraph" label="Computed loops" />
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
            <param name="maxLoopDistance" value="30000000" />