comparison chicViewpointBackgroundModel.xml @ 7:d3f74063cae4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788

6:12a6c7c4b00c

            --threads @THREADS@
            --outFileName background.txt
    ]]>    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_multiple_macro" />
        <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
        <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' />
        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' />
        <param argument='--truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros" help="Set this parameter if you want truncate zeros to fight over dispersion." />
    </inputs>
    <outputs>
        <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model" />
    </outputs>
    <tests>

7:d3f74063cae4

            --threads @THREADS@
            --outFileName background.txt
    ]]>    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_multiple_macro" />
        <param argument="--referencePoints" type="data" format="interval" label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
        <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help="Average the contacts of n bins via a sliding window approach." />
        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." />
        <param argument="--truncateZeros" type="boolean" truevalue="--truncateZeros" falsevalue="" checked="false" label="Truncate zeros" help="Set this parameter if you want truncate zeros to fight over dispersion." />
    </inputs>
    <outputs>
        <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model" />
    </outputs>
    <tests>