comparison pairedbamtobed.xml @ 0:6a2c228f93e3 draft default tip

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<tool id="pairedbamtobed12" name="Paired bam to bed12" version="0.1">
    <description>Paired Bam to Bed. With samtools sorting by name beforehand and back to required order for galaxy afterwards.</description>
    <requirements>
        <requirement type="package" version="1.0">pairedbamtobed12</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command>
    <![CDATA[
        samtools sort -n -O bam -T by_name        -o sorted_by_name.bam  "${input}" ;
        pairedBamToBed12 -i sorted_by_name.bam > "${output}"
    ]]>
    </command>
    <inputs>
        <param name="input" format="bam" label="Select BAM dataset to convert to bed" type="data" />
    </inputs>
    <outputs>
        <data format="bed" name="output" label="Bed12 version of ${on_string}" />
    </outputs>
    <tests>
        <!-- test data too large for toolshed 
             See: https://github.com/Christian-B/galaxy_shedtools/tree/master/pairedBamToBed12 -->
        <!--test>
            <param ftype="bam" name="input" value="filtered.bam" />
            <output file="paired.bed" ftype="bed" name="output" />
        </test-->
    </tests>
    <help>
<![CDATA[
This tools runs pairedbamtobed12 to convert a paired bam file to a bed file.

As pairedbamtobed12 requires a bam file sorted by name, while galaxy only allows ones sorted by alignment this tool first uses Samtools to reorder the bam file.


]]>
    </help>
    <citations>
        <citation type="bibtex">
            @misc{
                pairedBamToBed12,
                author = {Nicolas Bertin, Mickaël Mendez, Charles Plessy},
                title = {pairedBamToBed12 on GitHub},
                url = {https://github.com/Population-Transcriptomics/pairedBamToBed12}
            }
        </citation>
    </citations>
</tool>