comparison shuffleBed.xml @ 12:c782e0edc4f1 draft default tip

Uploaded

11:e526617a6bb9

<tool id="bedtools_shufflebed" name="ShuffleBed" version="0.2.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

            <when value="True">
                <param name="incl" type="data" format="bed" label="Choose File" />
            </when>
        </conditional>
        
        <param name="chromfirst" type="boolean" label="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size" selected="False" truevalue="-chromFirst" falsevalue="" />

        <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
        <param name="nooverlap" type="boolean" label="Don’t allow shuffled intervals to overlap" selected="False" truevalue="-noOverlapping" falsevalue="" />
        <param name="allowBeyond" type="boolean" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" />
    </inputs>
    <outputs>
        <data format="bed" name="output" />
        
    </outputs>
    <help>

**What it does**

12:c782e0edc4f1

<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

            <when value="True">
                <param name="incl" type="data" format="bed" label="Choose File" />
            </when>
        </conditional>
        
        <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 
            label="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size" />
        <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" />
        <param name="nooverlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" label="Don’t allow shuffled intervals to overlap" />
        <param name="allowBeyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" label="Allow the original the length of the original records to extebd beyond the length of the chromosome." />
    </inputs>
    <outputs>
        <data format="bed" name="output" />
    </outputs>
    <help>

**What it does**