# HG changeset patch
# User dfornika
# Date 1570224854 14400
# Node ID 2f02b158575774c5e671d02859f932edf2662884
# Parent  a2fa4a2588bceb7389386ba045f2d4a241568e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 9aca1f5531db1e71338919c63a4093c0b1e0cfd5-dirty

diff -r a2fa4a2588bc -r 2f02b1585757 unicycler.xml
--- a/unicycler.xml	Mon Sep 23 20:04:43 2019 -0400
+++ b/unicycler.xml	Fri Oct 04 17:34:14 2019 -0400
@@ -88,6 +88,9 @@
 #end if
 --kmer_count '$spades.kmer_count'
 --depth_filter '$spades.depth_filter'
+#if $graph_clean.largest_component
+    --largest_component
+#end if
 ## Rotation Options section
 ## ----------------------------------------------------------
 $rotation.no_rotate
@@ -163,6 +166,8 @@
             <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
             <param argument="--depth_filter" type="float" min="0" max="1" value="0.25"
                 label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
+	    <param argument="--largest_component" type="boolean" checked="false"
+                label="Only keep the largest connected component of the assembly graph"/>
         </section>
         <section name="rotation" expanded="false" title="Rotation options"
             help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
@@ -182,7 +187,7 @@
             <param argument="--min_component_size" type="integer" min="0" value="1000"
                 label="Unbridged graph components smaller than this size will be removed from the final graph" />
             <param argument="--min_dead_end_size" type="integer" min="0" value="1000"
-                label="Graph dead ends smaller than this size will be removed from the final graph"/>
+                   label="Graph dead ends smaller than this size will be removed from the final graph"/>
         </section>
         <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
             <param argument="--contamination" optional="true" type="data" format="fasta"