windowmasker_macros.xml

<macros>
    <xml name="requirements">
        <requirements>
        <!--
            Keep BLAST version in line with peterjc repo: https://github.com/peterjc/galaxy_blast
        -->
            <requirement type="package" version="2.7.1">blast</requirement>
	    <requirement type="package">perl</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @article{Morgulis_2005,
                    title={WindowMasker: window-based masker for sequenced genomes},
                    volume={22},
                    ISSN={1460-2059},
                    url={http://dx.doi.org/10.1093/bioinformatics/bti774},
                    DOI={10.1093/bioinformatics/bti774},
                    number={2}, journal={Bioinformatics},
                    publisher={Oxford University Press (OUP)},
                    author={Morgulis, A. and Gertz, E. M. and Schäffer, A. A. and Agarwala, R.},
                    year={2005}, month={Nov}, pages={134–141}
                }
            </citation>
            <citation type="bibtex">
                 @article{Cock_2015,
                    title={NCBI BLAST+ integrated into Galaxy},
                    volume={4},
                    ISSN={2047-217X},
                    url={http://dx.doi.org/10.1186/s13742-015-0080-7},
                    DOI={10.1186/s13742-015-0080-7},
                    number={1},
                    journal={GigaScience},
                    publisher={Oxford University Press (OUP)},
                    author={Cock, Peter J. A. and Chilton, John M. and Grüning, Björn and Johnson, James E. and Soranzo, Nicola},
                    year={2015}, month={Aug}
                }
            </citation>
            <yield />
        </citations>
    </xml>

    <!-- Helper function to add optional advanced parameters to command -->
    <token name="@OPTIONAL_PARAM_FUNC@">
<![CDATA[
        #def optional_param($_flag, $_flag_value, $_sep=" ")
            #if str($_flag_value) and str($_flag_value).strip():
                ${_flag}${_sep}${_flag_value}
            #end if
        #end def
]]>
    </token>
</macros>