comparison intersectBed.xml @ 20:df56e1b12d0c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a

19:a8eabd2838f6

<tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.0">
    <description>find overlapping intervals in various ways</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set inputBs = '" "'.join( [ str( $file ) for $file in $inputB ] )
        #set modes = ' '.join( str($overlap_mode).split(',') )

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

            -b "${inputBs}"
            $split
            $strand
            #if str($fraction) != "None" and str($fraction):
              -f "${fraction}"
            #end if
            $reciprocal
            $invert
            $once
            $header
            $modes
            $count
            > "${output}"
]]>
    </command>
    <inputs>
        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
        <param format="bed,bam,gff,vcf,gff3" name="inputB" type="data" multiple="True" label="One or more BAM/BED/GFF/VCF file(s)"/>
        <expand macro="strand2" />
        <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
            <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
            <option value="-wb">Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by the fraction- and reciprocal option (-wb)</option>
            <option value="-wo">Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by the fraction- and reciprocal option (-wo)</option>

            help="Alignments are only retained if the overlap with the an interval in the BED file comprises at least this fraction of the BAM alignment's length.  For example, to require that the overlap affects 50% of the BAM alignment, use 0.50. (-f)"/>
        <!-- -r -->
        <expand macro="reciprocal" />
        <!-- -v -->
        <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue=""
            label="Report only those alignments that **do not** overlap the BED file"
            help="(-v)"/>
        <!-- -u -->
        <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""
            label="Write the original A entry _once_ if _any_ overlaps found in B."
            help="Just report the fact >=1 hit was found. (-u)" />

20:df56e1b12d0c

<tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.1">
    <description>find overlapping intervals in various ways</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set modes = ' '.join( str($overlap_mode).split(',') )

        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:
                #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
                -b '$inputBs'
            #end if
            $split
            $strand
            #if str($fraction) != "None" and str($fraction):
              -f '${fraction}'
            #end if
            $reciprocal
            $invert
            $once
            $header
            $modes
            $count
            > '${output}'
]]>
    </command>
    <inputs>
        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="File A to intersect with B" help="BAM/BED/GFF/VCF format" />
        <conditional name="reduce_or_iterate">
            <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
                <option value='iterate' selected='true'>One output file per 'input B' file</option>
                <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option>
            </param>
            <when value='iterate'>
                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
                       label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
            </when>
            <when value='reduce'>
                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
                       label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
            </when>
        </conditional>
        <expand macro="strand2" />
        <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
            <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
            <option value="-wb">Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by the fraction- and reciprocal option (-wb)</option>
            <option value="-wo">Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by the fraction- and reciprocal option (-wo)</option>

            help="Alignments are only retained if the overlap with the an interval in the BED file comprises at least this fraction of the BAM alignment's length.  For example, to require that the overlap affects 50% of the BAM alignment, use 0.50. (-f)"/>
        <!-- -r -->
        <expand macro="reciprocal" />
        <!-- -v -->
        <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue=""
            label="Report only those alignments that **do not** overlap with file(s) B"
            help="(-v)"/>
        <!-- -u -->
        <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""
            label="Write the original A entry _once_ if _any_ overlaps found in B."
            help="Just report the fact >=1 hit was found. (-u)" />