comparison jasminesv.xml @ 1:2b62154e39c8 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit 600a9e3c1d884e5cf106e4477c7b8223ef105cdb"

0:630e2929a131

    'min_support=${min_support}'
    threads=\${GALAXY_SLOTS:-4}
    'spec_reads=${spec_reads}'
    'spec_len=${spec_len}'
    #if $dup_to_ins.dup_to_ins:
        'genome_file=reference.fa'
    #end if

    ## Flags:
    '${ignore_strand}'
    '${ignore_type}'

            <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
            <conditional name="dup_to_ins">
                <param name="dup_to_ins" value="--dup_to_ins"/>
                <conditional name="reference_source">
                    <param name="reference_source_selector" value="history"/>
                    <param name="ref_file" ftype="fasta" value="genome.fa"/>
                </conditional>
            </conditional>
            <output name="out_vcf" file="out1.vcf"/>
        </test>
        <test expect_num_outputs="1">

@REFERENCES@
    ]]></help>
    <expand macro="citations"/>
</tool>

1:2b62154e39c8

    'min_support=${min_support}'
    threads=\${GALAXY_SLOTS:-4}
    'spec_reads=${spec_reads}'
    'spec_len=${spec_len}'
    #if $dup_to_ins.dup_to_ins:
        'genome_file=reference'
    #end if

    ## Flags:
    '${ignore_strand}'
    '${ignore_type}'

            <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
            <conditional name="dup_to_ins">
                <param name="dup_to_ins" value="--dup_to_ins"/>
                <conditional name="reference_source">
                    <param name="reference_source_selector" value="history"/>
                    <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/>
                </conditional>
            </conditional>
            <output name="out_vcf" file="out1.vcf"/>
        </test>
        <test expect_num_outputs="1">

@REFERENCES@
    ]]></help>
    <expand macro="citations"/>
</tool>