<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
CrossMap.py bam
'${chain_source.input_chain}'
$optional_tags

-m $insert_size
-s $insert_size_stdev
-t $insert_size_fold

'${input}'
output
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM file"/>

        <expand macro="chain" />

        <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>

        <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
        <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
    </inputs>

    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" />
        <!-- CrossMap 0.2.5 does not produce output_unmapped -->
    </outputs>

    <tests>
        <test>
            <param name="index_source" value="history"/>
            <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
            <param name="include_fails" value="False"/>

            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
        </test>
        <test>
            <param name="index_source" value="cached"/>

            <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
            <param name="include_fails" value="False"/>

            <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
        </test>
    </tests>
    <help><![CDATA[
@HELP_GENERAL@

BAM
---------

CrossMap updates chromosomes, genome coordinates, header sections, and all
BAM flags accordingly. The program version (of CrossMap) is inserted into the
header section, along with the names of the original BAM file and the chain
file. For pair-end sequencing, insert size is also recalculated.


**Optional tags**

Q
    QC. QC failed.

N
    Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.

M
    Multiple mapped. Alignment can be liftover to multiple places.

U
    Unique mapped. Alignment can be liftover to only 1 place.

**Tags for pair-end sequencing include:**

QF
    QC failed
NN
    both read1 and read2 unmapped
NU
    read1 unmapped, read2 unique mapped
NM
    read1 unmapped, multiple mapped
UN
    read1 uniquely mapped, read2 unmap
UU
    both read1 and read2 uniquely mapped
UM
    read1 uniquely mapped, read2 multiple mapped
MN
    read1 multiple mapped, read2 unmapped
MU
    read1 multiple mapped, read2 unique mapped
MM
    both read1 and read2 multiple mapped

**Tags for single-end sequencing include**

QF
    QC failed
SN
    unmaped
SM
    multiple mapped
SU
    uniquely mapped
    ]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>
</tool>