# HG changeset patch
# User dereeper
# Date 1627322457 0
# Node ID 83e37d6aee5973fa618ef60b11f06776a660c96b
# Parent  35f0fcf77bdf0439d03cd979904fe0b1a53678fe
Uploaded

diff -r 35f0fcf77bdf -r 83e37d6aee59 ragoo.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ragoo.xml	Mon Jul 26 18:00:57 2021 +0000
@@ -0,0 +1,33 @@
+<tool id="ragoo" name="RaGOO" version="1.0">
+  <description>Order and assign scaffolds</description>
+ <requirements>
+  <requirement type="package" version="3.0.2">intervaltree</requirement>
+  <requirement type="package" version="1.21.1">numpy</requirement>
+  <requirement type="package" version="2.21">minimap2</requirement>
+ </requirements>
+
+  <command>perl ${__tool_directory__}/ragoo.pl $input $reference $output $output2
+</command>
+
+ 
+  <inputs>
+  <param format="fasta" name="input" type="data" label="Fasta file with contigs to be ordered and oriented: "/>
+  <param format="fasta" name="reference" type="data" label="Reference fasta file"/>
+   
+ </inputs>
+
+ <outputs>
+	 <data format="fasta" name="output" label="Fasta output of assigned scaffolds"/>
+	 <data format="fasta" name="output2" label="Fasta output of assigned scaffolds (without Chr0)"/>
+</outputs>
+
+  <help>
+ For full documentation, please go to the RaGOO website : https://github.com/malonge/RaGOO 
+	  
+</help>
+
+  <citations>
+	  <citation type="doi"> 10.1186/s13059-019-1829-6 </citation>
+
+  </citations>
+</tool>