view samtools_split.xml @ 0:5c2a97bb018b draft

Uploaded initial tool definition.

<tool id="samtools_split" name="Split" version="1.0.0">
    <description>a BAM file by read group</description>
    <requirements>
        <requirement type="package" version="1.1">samtools</requirement>
    </requirements>
    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
    <command><![CDATA[
        samtools split -f 'Read_Group_%!.bam'
        #if $header:
            -u "${output}":"${header}"
        #else:
            -u "${output}"
        #end if
        "${input_bam}"
        ]]></command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" multiple="true" />
        <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
     </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="phiX.bam" ftype="bam" />
            <output name="output" file="samtools_split_out.bam">
                <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
                <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
                <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
            </output>
        </test>
    </tests>
    <help>
**What it does**

This tool runs the ``samtools split`` command in the SAMtools toolkit.

Split BAM files by read group.

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_


If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
    </help>
</tool>