comparison bamtools.xml @ 6:e4490b16f0d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec

5:befc9dad4ca8

<tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>BAM datasets and perform other transformations</description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
        <![CDATA[
            ##set up input files
            ln -s '${input_bams}' localbam.bam &&
            ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai &&
            #if str( $analysis_type.analysis_type_selector ) == 'convert':
                #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':

                sort
                ${analysis_type.byname}
                -out '$out_file1'
            #end if
            -in localbam.bam
        ]]>
    </command>
    <inputs>
        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />
        <conditional name="analysis_type">
            <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
                <option value="convert">Convert</option>

6:e4490b16f0d7

<tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>BAM datasets and perform other transformations</description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.16.1">samtools</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
            ##set up input files
            ln -s '${input_bams}' localbam.bam &&
            ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai &&
            #if str( $analysis_type.analysis_type_selector ) == 'convert':
                #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':

                sort
                ${analysis_type.byname}
                -out '$out_file1'
            #end if
            -in localbam.bam
    ]]></command>
    <inputs>
        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />
        <conditional name="analysis_type">
            <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
                <option value="convert">Convert</option>