# HG changeset patch
# User Michael R. Crusoe <mcrusoe@msu.edu>
# Date 1407351051 14400
# Node ID 2c03c19808c5ff187d4d2e791d01b39ea30c3bb5
# Parent  3d65329a491dc07d2fa8c39f5d1f85dca1dfe386
Add citations

diff -r 3d65329a491d -r 2c03c19808c5 abundance-dist-single.xml
--- a/abundance-dist-single.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/abundance-dist-single.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -91,7 +91,10 @@
 	    </test>
 
     </tests>
-    
+    <citations>
+	<expand macro="software-citation" />
+	<expand macro="counting-citation" />
+    </citations>
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <!--
 	<help>
diff -r 3d65329a491d -r 2c03c19808c5 abundance-dist.xml
--- a/abundance-dist.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/abundance-dist.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -61,7 +61,10 @@
                     	</output>
             	</test>
     	</tests>
-    
+	<citations>
+		<expand macro="software-citation" />
+		<expand macro="counting-citation" />
+	</citations>
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <!--
 	<help>
diff -r 3d65329a491d -r 2c03c19808c5 do-partition.xml
--- a/do-partition.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/do-partition.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -100,6 +100,10 @@
 
 	</tests>
     -->
+	<citations>
+		<expand macro="software-citation" />
+		<expand macro="graph-citation" />
+	</citations>
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <!--
 	<help>
diff -r 3d65329a491d -r 2c03c19808c5 extract-partitions.xml
--- a/extract-partitions.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/extract-partitions.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -67,6 +67,10 @@
 		</test>
 
 	</tests>
+	<citations>
+		<expand macro="software-citation" />
+		<expand macro="graph-citation" />
+	</citations>
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <!--
 	<help>
diff -r 3d65329a491d -r 2c03c19808c5 filter-abund.xml
--- a/filter-abund.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/filter-abund.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -77,6 +77,10 @@
                         </output>
                 </test>
         </tests> 
+	<citations>
+		<expand macro="software-citation" />
+		<expand macro="counting-citation" />
+	</citations>
 	<!-- [OPTIONAL] ReST Help displayed in Galaxy -->
     <!--
 	<help>
diff -r 3d65329a491d -r 2c03c19808c5 filter-below-abund.xml
--- a/filter-below-abund.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/filter-below-abund.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -56,6 +56,10 @@
                         </output>
                 </test>
 	</tests> -->
+	<citations>
+		<expand macro="software-citation" />
+		<expand macro="counting-citation" />
+	</citations>
 	<!-- [OPTIONAL] ReST Help displayed in Galaxy -->
     <!--
 	<help>
diff -r 3d65329a491d -r 2c03c19808c5 macros.xml
--- a/macros.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/macros.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -119,4 +119,16 @@
                         checked="true" 
                         help="Output zero count bins" />
 	</xml>
-`</macros>
+	<xml name="software_citation" type="doi">10.6084/m9.figshare.979190</xml>
+	<xml name="diginorm-citation" type="bibtex">@misc{diginorm,
+    Author = {Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
+Alexis B and Brom, Timothy H},
+    Title = {A Reference-Free Algorithm for Computational Normalization of
+Shotgun Sequencing Data},
+    Year = {2012},
+    Eprint = {arXiv:1203.4802},
+}</xml>
+	<xml name="graph-citation" type="doi">10.1073/pnas.1121464109</xml>
+	<xml name="counting-citation" type="doi">10.1371/journal.pone.0101271</xml>
+
+</macros>
diff -r 3d65329a491d -r 2c03c19808c5 normalize-by-median.xml
--- a/normalize-by-median.xml	Tue Aug 05 17:30:32 2014 -0400
+++ b/normalize-by-median.xml	Wed Aug 06 14:50:51 2014 -0400
@@ -124,7 +124,10 @@
 		</test>
 
 	</tests>
-    
+	<citations>
+		<expand macro="software-citation" />
+		<expand macro="diginorm-citation" />
+	</citations>
     <!-- [OPTIONAL] Help displayed in Galaxy -->
     <!--
 	<help>