comparison annotateBed.xml @ 4:607c0576c6ab draft

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

3:2cd7e321d259

<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools annotate
        -i "${inputA}"
        #if $names.names_select == 'yes':
            -files
            #for $bed in $names.beds:

                "${bed.inputName}"
            #end for
        #else:
            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
            -files "${files}"
        #end if
        $strand
        $counts
        $both
        > "${output}"

4:607c0576c6ab

<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1">
    <description>annotate coverage of features from multiple files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[

        bedtools annotate
        -i "${inputA}"
        #if $names.names_select == 'yes':
            -files
            #for $bed in $names.beds:

                "${bed.inputName}"
            #end for
        #else:
            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
            -files "${files}"
            #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
            -names "${names}"
        #end if
        $strand
        $counts
        $both
        > "${output}"