<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.9</token>
    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
        ##prepare input and indices 
        #for $i, $bam in enumerate( $input_bams ):
            ln -s '$bam' '${i}' &&
            #if $bam.is_of_type('bam'):
                #if str( $bam.metadata.bam_index ) != "None":
                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
                #else:
                    samtools index '${i}' '${i}.bai' &&
                #end if
            #elif $bam.is_of_type('cram'):
                #if str( $bam.metadata.cram_index ) != "None":
                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
                #else:
                    samtools index '${i}' '${i}.crai' &&
                #end if
            #end if
        #end for
    ]]></token>
    <xml name="flag_options">
        <option value="1">read is paired</option>
        <option value="2">read is mapped in a proper pair</option>
        <option value="4">read is unmapped</option>
        <option value="8">mate is unmapped</option>
        <option value="16">read reverse strand</option>
        <option value="32">mate reverse strand</option>
        <option value="64">read is the first in a pair</option>
        <option value="128">read is the second in a pair</option>
        <option value="256">alignment or read is not primary</option>
        <option value="512">read fails platform/vendor quality checks</option>
        <option value="1024">read is a PCR or optical duplicate</option>
        <option value="2048">supplementary alignment</option>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/},}
            </citation>
            <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">
                @misc{Danecek_et_al,
                Author={Danecek, P., Schiffels, S., Durbin, R.},
                title={Multiallelic calling model in bcftools (-m)},
                url = {http://samtools.github.io/bcftools/call-m.pdf},}
            </citation>
            <citation type="bibtex">
                @misc{Durbin_VCQC,
                Author={Durbin, R.},
                title={Segregation based metric for variant call QC},
                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
            </citation>
            <citation type="bibtex">
                @misc{Li_SamMath,
                Author={Li, H.},
                title={Mathematical Notes on SAMtools Algorithms},
                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
            </citation>
            <citation type="bibtex">
                @misc{SamTools_github,
                title={SAMTools GitHub page},
                url = {https://github.com/samtools/samtools},}
            </citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error" />
        </stdio>
    </xml>
    <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>