comparison braker3.xml @ 5:3452c806c478 draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 5bcf6a26284965f4fbf04be67ae7c186bb7e908f

4:96ad8f880755

## This specific GeneMark version has some tools bundled with it, forced to use it.
## I feel dirty. Pardon me.

export PATH="\$GENEMARK_PATH/../tools/:\$PATH" &&

braker.pl
--genome '${genome}'
$softmasking

#if $evidences.bam:

        </data>
        <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: GFF Annotation" from_work_dir="braker/braker.gff3">
            <filter>output_format == 'gff3'</filter>
        </data>
    </outputs>
    
    <tests>
        <test expect_failure="true">
            <param name="genome" value="genome_masked.fa"/>
            <section name="evidences">
                <param name="bam" value="SRR7458692.bam"/>

            </section>
            <param name="output_format" value="gff3" />
            <output name="output_gff" file="out_genome/braker.gff3"/>
        </test> -->

    
    <help><![CDATA[

Braker3_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.

In contrast to other available methods that rely on protein homology information, BRAKER3 reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.

5:3452c806c478

## This specific GeneMark version has some tools bundled with it, forced to use it.
## I feel dirty. Pardon me.

export PATH="\$GENEMARK_PATH/../tools/:\$PATH" &&

## Copy Augustus config dir to work dir, to make sure it's writable when running with containers
cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&

braker.pl
--genome '${genome}'
$softmasking

#if $evidences.bam:

        </data>
        <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: GFF Annotation" from_work_dir="braker/braker.gff3">
            <filter>output_format == 'gff3'</filter>
        </data>
    </outputs>

    <tests>
        <test expect_failure="true">
            <param name="genome" value="genome_masked.fa"/>
            <section name="evidences">
                <param name="bam" value="SRR7458692.bam"/>

            </section>
            <param name="output_format" value="gff3" />
            <output name="output_gff" file="out_genome/braker.gff3"/>
        </test> -->


    <help><![CDATA[

Braker3_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.

In contrast to other available methods that rely on protein homology information, BRAKER3 reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.