--- a/macros.xml	Thu Sep 27 17:52:13 2018 -0400
+++ b/macros.xml	Sat Jan 29 12:49:28 2022 +0000
@@ -1,22 +1,39 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-        <requirement type="package" version="2.0">wtdbg</requirement>
-            <yield/>
-        </requirements>
-    </xml>
-    <xml name="citations">
-        <citations>
-            <citation type="bibtex">
-@misc{githubwtdbg-2,
-  author = {Ruan, Jue},
-  year = {2018},
-  title = {wtdbg-2},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/ruanjue/wtdbg2},
-}</citation>
-            <yield />
-        </citations>
-    </xml>
-</macros>
+<macros>
+    <token name="@TOOL_VERSION@">2.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">doi:10.1038/s41592-019-0669-3</citation>
+        </citations>
+    </xml>
+    <token name="@ASM_OPTIONS@">
+        -X $asm.X
+        -L $asm.L
+        -k $asm.k
+        -p $asm.p
+        -K $asm.K
+        -s $asm.s
+        -e $asm.e
+        $asm.realign
+        $asm.contained_reads
+    </token>
+    <token name="@CNS_OPTIONS@">
+        -j $cns.j
+        -M $cns.M
+        -X $cns.X
+        -I $cns.I
+        -D $cns.D
+        -b $cns.b
+        -H $cns.H
+        -B $cns.B
+        -W $cns.W
+        -w $cns.w
+        -A $cns.A
+        -S $cns.S
+        -R $cns.R
+        -c $cns.c
+        -C $cns.C
+        -F $cns.F
+        -N $cns.N
+    </token>
+</macros>