comparison intersectBed.xml @ 37:ce3c7f062223 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"

36:0a5c785ac6db

#if $modes == "None":
    #set modes = ''
#end if

bedtools intersect
#if $inputA.is_of_type('bam'):
    -abam '${inputA}'
#else:
    -a '${inputA}'
#end if

#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
    -b '$reduce_or_iterate.inputB'
#else:
    -b

#end if
$invert
$once
$header
$modes
$sorted
#if str($sorted) != '':
    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
    #end if
#end if
$bed
$count
> '${output}'
    ]]></command>
    <inputs>

        <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
            label="For each entry in A, report the number of overlaps with B."
            help="Reports 0 for A entries that have no overlap with B" />
        <!-- -bed -->
        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
            label="When using BAM input (-abam), write output as BED instead of BAM." />
        <!-- -sorted -g  -->
        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled." />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA">
            <change_format>

37:ce3c7f062223

#if $modes == "None":
    #set modes = ''
#end if

bedtools intersect
-a '${inputA}'

#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
    -b '$reduce_or_iterate.inputB'
#else:
    -b

#end if
$invert
$once
$header
$modes
@SORTED@
$bed
$count
> '${output}'
    ]]></command>
    <inputs>

        <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
            label="For each entry in A, report the number of overlaps with B."
            help="Reports 0 for A entries that have no overlap with B" />
        <!-- -bed -->
        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
            label="When using BAM input, write output as BED instead of BAM." />
        <!-- -sorted -g  -->
        <expand macro="sorted" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format_source="inputA" metadata_source="inputA">
            <change_format>