<tool id="crossmap_gff" name="CrossMap GFF" 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 gff
'${chain_source.input_chain}'
'${input}'

#if str($include_fails) == "True"
    >
#end if

output
    ]]></command>

    <inputs>
        <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>

        <expand macro="chain" />

        <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
    </inputs>

    <outputs>
        <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
            <param name="index_source" value="history"/>
            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
            <param name="include_fails" value="False"/>

            <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
        </test>
        <test>
            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
            <param name="index_source" value="history"/>
            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
            <param name="include_fails" value="True"/>

            <output name="output" file="test_gff_01_output_a__all.gtf"/>
        </test>
        <test><!-- cached chain file -->
            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf" dbkey="hg18"/>
            <param name="index_source" value="cached"/>
            <param name="include_fails" value="True"/>

            <output name="output" file="test_gff_01_output_a__all.gtf"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_GENERAL@

GFF / GTF
---------
Your input data should be either GTF/GFF2.5 or GFF3 format.

GFF (General Feature Format) is another plain text file used to describe
gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
first eight fields are the same as GFF. Only chromosome and genome
coordinates are updated. The format of output is determined from the input.

Notes:

- Each feature (exon, intron, UTR, etc) is processed separately and
  independently, and we do NOT check if features originally belonging to
  the same gene were converted into the same gene.
- If user want to liftover gene annotation files, use BED12 format.
    ]]></help>

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