# HG changeset patch
# User iuc
# Date 1499351443 14400
# Node ID a9098353ae22dcc554b99afbd77a5f576237e3ca
# Parent  e02e9af2743fc87fa87f7a9ac26e4562c33a1b73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 0c61b60404e4e1dfb5be4fb2fd310f9f3606c7a6

diff -r e02e9af2743f -r a9098353ae22 roary.xml
--- a/roary.xml	Fri Jun 23 07:53:29 2017 -0400
+++ b/roary.xml	Thu Jul 06 10:30:43 2017 -0400
@@ -44,6 +44,7 @@
       <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/>
       
       <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced.">
+        <option value="abg_nw">Accessory binary genes in newick format</option>
         <option value="abg_fa">Accessory binary genes in fasta format</option>
         <option value="accgraph">Accessory graph in dot format</option>
         <option value="acchead_embl">Accessory header file in embl format</option>
@@ -76,6 +77,9 @@
       <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" >
         <filter>outputs and 'abg_fa' in outputs</filter>
       </data>
+      <data format="nhx" name="acc_bin_new" label="${tool.name} on ${on_string} Accessory Binary Genes (Newick)" from_work_dir="out/accessory_binary_genes.fa.newick" >
+        <filter>outputs and 'abg_nw' in outputs</filter>
+      </data>
       <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
         <filter>outputs and 'accgraph' in outputs</filter>
       </data>