view macros.xml @ 5:f57df915aa10 draft

planemo upload for repository commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:39 -0400
parents af7c50162f0b
children 88eedb4abea0
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    <xml name="requirements">
            <requirement type="package" version="1.3.1">samtools</requirement>
    <token name="@TOOL_VERSION@">1.3.1</token>
    <xml name="citations">
            <citation type="bibtex">
                title={Definition of SAM/BAM format},
                url = {},}
            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
            <citation type="bibtex">
                Author={Danecek, P., Schiffels, S., Durbin, R.},
                title={Multiallelic calling model in bcftools (-m)},
                url = {},}
            <citation type="bibtex">
                Author={Durbin, R.},
                title={Segregation based metric for variant call QC},
                url = {},}
            <citation type="bibtex">
                Author={Li, H.},
                title={Mathematical Notes on SAMtools Algorithms},
                url = {},}
            <citation type="bibtex">
                title={SAMTools GitHub page},
                url = {},}
    <xml name="version_command">
        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
    <xml name="stdio">
            <exit_code range="1:" level="fatal" description="Error" />
    <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.