<tool id="samtools_index" name="Samtools index" version="2.0.4" profile="@PROFILE@">
    <description>order of storing aligned sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
	@ADDMEMORY@
        samtools index
            -@ \$addthreads
            -m \$addmemory"M"
            $prim_key_cond.prim_key_select
            '${input1}'
            '${output1}'
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
        <conditional name="prim_key_cond">
            <param name="prim_key_select" type="select" label="Index type">
                <option value="-b" selected="True">BAI (-b)</option>
                <option value="-c" selected="True">CSI (-c)</option>
            </param>
            <when value="-b"/>
            <when value="-c"/>
        </conditional>
    </inputs>
    <outputs>
       <data name="output1" format="bam">
            <change_format>
                <when input="prim_key_cond.prim_key_select" value="-b" format="bai" />
                <when input="prim_key_cond.prim_key_select" value="-c" format="csi" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bam" ftype="bam" />
            <param name="prim_key_cond.prim_key_select" value="-c" />
            <output name="output1" file="1.bam.bai" ftype="bai" lines_diff="4" />
        </test>
    </tests>
    <help>
**What it does**

Indexes a BAM file 
    </help>
    <expand macro="citations"/>
</tool>