# HG changeset patch
# User iuc
# Date 1576700686 18000
# Node ID 1aed170afb2bb70dea86cacff14ff981f5a8922a
# Parent  649b98adce777a70d05e31e175faeb6928e429c5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit c39323361ef6ba2664646e4476736c80bcd01124"

diff -r 649b98adce77 -r 1aed170afb2b orthofinder_only_groups.xml
--- a/orthofinder_only_groups.xml	Tue Mar 06 11:10:03 2018 -0500
+++ b/orthofinder_only_groups.xml	Wed Dec 18 15:24:46 2019 -0500
@@ -2,8 +2,9 @@
     <description>finds orthogroups in a set of proteomes</description>
     <requirements>
         <requirement type="package" version="2.1.2">orthofinder</requirement>
+        <requirement type="package" version="2.34">util-linux</requirement>
     </requirements>
-    <command>
+    <command detect_errors="exit_code">
     <![CDATA[
         ## prepare inputs
         #if $init.start == "fasta":
@@ -400,7 +401,7 @@
 ======================
 
 Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md
-Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-options.pdf
+Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf
 
 OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).