<commit_before><tool id="samtools_sort" name="Samtools sort" version="2.0.2">
    <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 sort
            -@ \$addthreads
            -m \$addmemory"M"
            ###if str(compression):
            ##    -l '$compression'
            ###end if
            $prim_key_cond.prim_key_select
            #if $prim_key_cond.prim_key_select == '-t':
                $prim_key_cond.tag
                $prim_key_cond.sec_key_select
            #end if
            -O bam
            -T sorttmp
            '${input1}'
             > '${output1}'
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="sam,bam,cram" label="BAM File" />
        <conditional name="prim_key_cond">
            <param name="prim_key_select" type="select" label="Primary sort key">
                <option value="">coordinate</option>
                <option value="-n">name (-n)</option>
                <option value="-t">tag (-t)</option><commit_msg>Changed bam to unsorted.bam as input formats in order to support all BAM variants<commit_after><tool id="samtools_sort" name="Samtools sort" version="2.0.2">
    <description>order of storing aligned sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
	@ADDMEMORY@
        samtools sort
            -@ \$addthreads
            -m \$addmemory"M"
            ###if str(compression):
            ##    -l '$compression'
            ###end if
            $prim_key_cond.prim_key_select
            #if $prim_key_cond.prim_key_select == '-t':
                $prim_key_cond.tag
                $prim_key_cond.sec_key_select
            #end if
            -O bam
            -T sorttmp
            '${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="Primary sort key">
                <option value="">coordinate</option>
                <option value="-n">name (-n)</option>
                <option value="-t">tag (-t)</option>
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