comparison macros.xml @ 4:607c0576c6ab draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316

3:2cd7e321d259

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.22">bedtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">2.22</token>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <exit_code range=":-1" />

            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
    </xml>
    <xml name="genome">
        <param format="tabular" name="genome" type="data" label="Genome file" />
        <!--TODO: make use of: ${chromInfo} -->
    </xml>
    <xml name="addition">
        <conditional name="addition">
            <param name="addition_select" type="select" label="Choose what you want to do">
                <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option>

4:607c0576c6ab

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.24">bedtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">2.24</token>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <exit_code range=":-1" />

            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
    </xml>
    <xml name="genome">
        <param format="tabular" name="genome" type="data" label="Genome file" />
        <!--TODO: make use of: ${chromInfo} -->
    </xml>
    <xml name="closest_D_option">
        <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
            label="Ignore features in B that are upstream of features in A" 
            help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />

        <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
            label="Ignore features in B that are downstream of features in A" 
            help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />

        <param name="fu" type="boolean" checked="false" truevalue="-fu" falsevalue=""
            label="Choose first from features in B that are upstream of features in A" 
            help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-fu)" />

        <param name="fd" type="boolean" checked="false" truevalue="-fd" falsevalue=""
            label="Choose first from features in B that are downstream of features in A" 
            help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-fd)" />
    </xml>
    <xml name="addition">
        <conditional name="addition">
            <param name="addition_select" type="select" label="Choose what you want to do">
                <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option>