--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/windowmasker_macros.xml	Tue May 16 13:18:12 2017 -0400
@@ -0,0 +1,55 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+        <!--
+            Use older version of NCBI BLAST+ because 2.6.0 is available
+            through bioconda but not through the Galaxy toolshed
+        -->
+            <requirement type="package" version="2.5.0">blast</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>