view macros.xml @ 8:71d5c34fef4e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

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                @misc{SAM_def,
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            <citation type="doi">10.1093/bioinformatics/btr509</citation>
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                @misc{Danecek_et_al,
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                title={Multiallelic calling model in bcftools (-m)},
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                @misc{Durbin_VCQC,
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                @misc{Li_SamMath,
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                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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    <xml name="version_command">
        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error" />
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    <token name="@no-chrom-options@">
-----

.. class:: warningmark

**No options available? How to re-detect metadata**

If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:

1. Click on the **pencil** icon adjacent to the dataset in the history
2. A new menu will appear in the center pane of the interface
3. Click **Datatype** tab
4. Set **New Type** to **BAM**
5. Click **Save**

The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
    </token>
</macros>