<tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0">
    <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[
        #if $input_file.extension == "bam":
            #set $input_file = "input.sam"
            samtools view -h '${seq_source.input}' > '${input_file}' &&
        #else:
            #set $input_file = "input.bam"
            ln -s '${seq_source.input}' '${input_file}'
        #end if

        CrossMap.py
            bam

            "$chain_source.input_chain"
            $optional_tags

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

            '${input_file}'
            '${output}'

            && samtools sort "${output}.sam" > '${output}'
            && samtools sort "${output}.unmap.sam" > '${output_unmapped}'
    ]]></command>

    <inputs>
        <conditional name="seq_source">
            <expand macro="source" />
            <when value="cached">
                <param type="data" format="bam" name="input" label="BAM file">
                    <validator type="unspecified_build"/>
                    <!-- Gives error in tests
                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
                    -->
                </param>
                <param name="input_chain" type="select" label="Lift Over To">
                    <options from_file="liftOver.loc">
                        <column name="name" index="1"/>
                        <column name="value" index="2"/>
                        <column name="dbkey" index="0"/>
                        <filter type="data_meta" ref="input" key="dbkey" column="0"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param type="data" format="bam" name="input" label="BAM/SAM file"/>
                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
            </when>
        </conditional>
        <expand macro="chain" />
        <param name="optional_tags" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM/SAM Headers" argument="-a"/>

        <param name="insert_size" type="float" value="200.0" label="Insert size" argument="-m" help="Average insert size of pair-end sequencing (bp) [default=200.0]"/>
        <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev" argument="-s" help="Stanadard deviation of insert size. [default=30.0]"/>
        <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange" argument="-t" 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. [default=3.0]"/>
</inputs>

    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
        <data format="bam" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" />
    </outputs>

    <tests>
    <!-- BAM/SAM -->
        <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" compare="diff" lines_diff="8"/>
            <output name="output_unmapped" file="test_bam_01_output_a.unmap.bam" compare="diff" lines_diff="8"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_GENERAL@

SAM / BAM
---------

    CrossMap updates chromosomes, genome coordinates, header sections, and all
    SAM 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

See `the manual <http://crossmap.sourceforge.net/#convert-bam-sam-format-files>`__ for more details
]]></help>

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