comparison braker3.xml @ 3:5460380cc057 draft

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 66b1967152f63ef95eee2058d768a5ae92502997

2:bbe51a1c2b6b

## 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" &&

## GeneMark only search for license in ~/.gm_key
cp '${genemark_license}' ~/.gm_key &&

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

#if $evidences.bam:
    --bam ${evidences.bam}
#end if

--threads  \${GALAXY_SLOTS:-2}
--useexisting
]]></command>
    <inputs>
        <param name="genemark_license" type="data" format="txt" label="GeneMark license file" help="Braker uses GeneMark, which is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators." />

        <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should preferably be soft-masked (with RepeatMasker for example)" />

        <param argument="--softmasking" type="boolean" checked="true" truevalue="" falsevalue="--softmasking_off" label="Genome sequence is soft-masked" />

        <param argument="--species" type="text" label="Species name" optional="true" help="Using Sp_1, if no species is assigned"/>

            <option value="gff3">GFF3</option>
        </param>
    </inputs>

    <outputs>
        <data name='output_gtf' format='gtf' label="GTF Annotation" from_work_dir="braker/braker.gtf">
            <filter>output_format == 'gtf'</filter>
        </data>
        <data name='output_gff' format='gff3' label="GFF Annotation" from_work_dir="braker/braker.gff3">
            <filter>output_format == 'gff3'</filter>
        </data>
    </outputs>
    
    <tests>
        <test expect_failure="true">
            <param name="genemark_license" value="gm_key_64"/>
            <param name="genome" value="genome_masked.fa"/>
            <section name="evidences">
                <param name="bam" value="SRR7458692.bam"/>
            </section>
            <param name="output_format" value="gtf" />
        </test>
    </tests>

    <!-- <test expect_num_outputs="1">
            <param name="genemark_license" value="gm_key_64" />
            <param name="genome" value="genome_masked.fa" />
            <section name="augustus">
                <param name="rounds" value="2" />
            </section>
            <section name="evidences">

3:5460380cc057

## 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:
    --bam ${evidences.bam}
#end if

--threads  \${GALAXY_SLOTS:-2}
--useexisting
]]></command>
    <inputs>
        <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should preferably be soft-masked (with RepeatMasker for example)" />

        <param argument="--softmasking" type="boolean" checked="true" truevalue="" falsevalue="--softmasking_off" label="Genome sequence is soft-masked" />

        <param argument="--species" type="text" label="Species name" optional="true" help="Using Sp_1, if no species is assigned"/>

            <option value="gff3">GFF3</option>
        </param>
    </inputs>

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

    <!-- <test expect_num_outputs="1">
            <param name="genome" value="genome_masked.fa" />
            <section name="augustus">
                <param name="rounds" value="2" />
            </section>
            <section name="evidences">