comparison coverageBed.xml @ 29:6bb3cd018203 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b

28:6283d16e40ed

<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.2">
    <description>of features in file B on the features in file A (bedtools coverage)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        $a_or_b
        -a '$inputA'
        #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
            -b '$reduce_or_iterate.inputB'
            #if $reduce_or_iterate.inputB.is_of_type('bam'):
                -sorted  -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
            #end if
        #else:
            #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
            -b '$inputBs'
        #end if

            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
            <param name="overlap_b" value="1"  />
            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
        </test>

29:6bb3cd018203

<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.3">
    <description>of features in file B on the features in file A (bedtools coverage)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        $a_or_b
        -a '$inputA'
        #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
            -b '$reduce_or_iterate.inputB'
            #if $reduce_or_iterate.inputB.is_of_type('bam'):
                -sorted  -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' |  sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
            #end if
        #else:
            #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
            -b '$inputBs'
        #end if

            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="multiCov1.bed" ftype="bed" />
            <param name="inputB" value="srma_in3.bam" ftype="bam" />
            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="multiCov1.bed" ftype="bed" />
            <param name="reduce_or_iterate_selector" value="reduce" />
            <param name="inputB" value="srma_in3.bam" ftype="bam" />
            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
            <param name="overlap_b" value="1"  />
            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
        </test>