comparison macs2_callpeak.xml @ 15:c33686854b19 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786

14:c16dbe4e2db2

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">

        ## advanced options

        $advanced_options.nolambda
        $advanced_options.to_large

        #if $advanced_options.ratio:
            --ratio $advanced_options.ratio
        #end if

                <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
                    label="When set, scale the small sample up to the bigger sample"
                    help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. (--to-large). Default: No"/>
                <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/>
                <param name="ratio" type="float" optional="True"
                    label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
                    help="(--ratio) Default: ignore"/>
                <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
                    help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal). Default: 1000"/>

15:c33686854b19

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.5" profile="17.09">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">

        ## advanced options

        $advanced_options.nolambda
        $advanced_options.to_large
        $advanced_options.spmr

        #if $advanced_options.ratio:
            --ratio $advanced_options.ratio
        #end if

                <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
                    label="When set, scale the small sample up to the bigger sample"
                    help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. (--to-large). Default: No"/>
                <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/>
                <param name="spmr" type="boolean" truevalue="--SPMR" falsevalue="" checked="False" optional="True"
                    label="Save signal per million reads for fragment pileup profiles"
                    help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. (--SPMR). Default: No"/>
                <param name="ratio" type="float" optional="True"
                    label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
                    help="(--ratio) Default: ignore"/>
                <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
                    help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal). Default: 1000"/>