comparison macros.xml @ 12:542d2008a462 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 344140b8df53b8b7024618bb04594607a045c03a

11:76c128f4cef9

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

            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>
    <xml name="reciprocal">
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require that the fraction of overlap be reciprocal for A and B"
            help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" />

            </when>
            <when value="False" />
        </conditional>
    </xml>
    <xml name="split">
        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" 
            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 
            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} -->

12:542d2008a462

    <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" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
        <version_command>bedtools --version</version_command>
    </xml>
    <xml name="reciprocal">
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
            label="Require that the fraction of overlap be reciprocal for A and B"
            help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" />

            </when>
            <when value="False" />
        </conditional>
    </xml>
    <xml name="split">
        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
            label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
            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} -->