view Sambamba_merge.xml @ 0:305a4f796bd3 draft default tip

planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9

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−<tool id="sambamba_merge" name="Sambamba merge" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
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−    <description>Merge several BAM files into one</description>
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−    <macros>
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−        <import>macros.xml</import>
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−    </macros>
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−    <expand macro="requirements"/>
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−    <command><![CDATA[
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−        sambamba merge
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−            -l $compression_level
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−            '${output}'
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−            #for $infile in $input_bam:
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−                '${infile}'
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−            #end for
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−            --nthreads \${GALAXY_SLOTS:-8}
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−    ]]></command>
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−    <inputs>
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−        <param name="input_bam" type="data" format="qname_sorted.bam,bam" multiple="true" label="Input BAM files to be merged" help="Please note that the sorting order of all input files must be the same"/>
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−        <param argument="--compression-level" type="integer" value="5" min="0" max="9" label="Level of compression for merged BAM file, number from 0 to 9"/>
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−    </inputs>
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−    <outputs>
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−        <data name="output" format_source="input_files"/>
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−    </outputs>
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−    <tests>
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−        <test expect_num_outputs="1">
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−            <param name="input_bam" value="qname_sorted.bam,qname_sorted.bam"/>
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−            <param name="compression_level" value="5"/> 
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−            <output name="output" file="qname_sorted_merged.bam" lines_diff="4"/>
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−        </test>
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−        <test expect_num_outputs="1">
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−            <param name="input_bam" value="coordinate_sorted.bam,coordinate_sorted.bam"/>
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−            <param name="compression_level" value="5"/>  
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−            <output name="output" file="coordinate_sorted_merged.bam" lines_diff="4"/>
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−        </test>
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−    </tests>
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−    <help>
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−<![CDATA[
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−
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−sambamba_merge is used to merge several sorted BAM files into one. The sorting order of all the files must be the same, and it is maintained in the output file.
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−
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−SAM headers are merged automatically like in Picard merging tool.
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−]]>
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−    </help>
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−    <expand macro="citations" />
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−</tool>