view samtools_bedcov.xml @ 0:6ffa7e68dc1f draft

Uploaded initial tool definition.

<tool id="samtools_bedcov" name="Calculate read depth" version="1.0.0">
    <description>on BAM files</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[
        for bamfile in 
        #for dataset in $input_bams:
            "${dataset}"
        #end for
        ; do
            if [ ! -f \$bamfile.bai ] ; then
                ln -s \$bamfile && samtools index `basename \$bamfile` ;
            else
                ln -s \$bamfile && ln -s \$bamfile.bai ;
            fi ;
        done ;
        samtools bedcov "${input_bed}"
        #for dataset in $input_bams:
            `basename "${dataset}"`
        #end for
        > "${output}"
        ]]></command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <inputs>
        <param name="input_bed" type="data" format="bed" label="BED file" />
        <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
            <output name="output" file="samtools_bedcov_out1.tab" />
        </test>
        <test>
            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
            <output name="output" file="samtools_bedcov_out2.tab" />
        </test>
    </tests>
    <help>
**What it does**

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

Show read depth per BED region.

**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>