comparison crossmap_gff.xml @ 9:040eed862c91 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622

8:45c57bf42470

<tool id="crossmap_gff" name="CrossMap GFF" version="@WRAPPER_VERSION@-0">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

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

'${output}'
    ]]></command>

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

        <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}" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>

- 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>

9:040eed862c91

<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"/>

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

output
    ]]></command>

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

        <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"/>

- 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>