diff pplacer.xml @ 6:3c50a937d7c1 draft

Uploaded

--- a/pplacer.xml	Thu Mar 26 16:56:09 2015 -0400
+++ b/pplacer.xml	Wed Apr 15 19:14:23 2015 -0400
@@ -1,18 +1,18 @@
 <tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0">
   <description>on a reference tree</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
   <requirements>
     <requirement type="package">yapp_env</requirement>
   </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
+  <stdio>
+    <expand macro="basic_errors"/>
+  </stdio>
   <version_command>echo "pplacer $(pplacer --version)"</version_command>
   <command interpreter="bash">
     pplacer-wrapper.sh ${config}
   </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
   <inputs>
     <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
     <param name="query_seqs" type="data" format="fasta" label="Query alignment"/>
@@ -41,13 +41,8 @@
 according to a reference alignment, producing taxonomic annotations which can
 be used for classification and visualization.
 
------
-
-**Citation**
-
-Matsen F, Kodner R, Armbrust E V: **pplacer: linear time maximum-likelihood and
-Bayesian phylogenetic placement of sequences onto a fixed reference tree**. BMC
-Bioinformatics 2010, **11**:1.
-
   </help>
+  <citations>
+    <expand macro="cite_pplacer"/>
+  </citations>
 </tool>