# HG changeset patch
# User thanhlv
# Date 1629641825 0
# Node ID 931aefbda8d5c0317c0b0805f29c664dc449f93e
# Parent  13ed2ccb0fb205c967740fd418c746254d708056
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/flye commit 23b5fdb26887ca1a7f320a5f87981d1bab7a8de7-dirty"

diff -r 13ed2ccb0fb2 -r 931aefbda8d5 flye.xml
--- a/flye.xml	Thu Aug 06 14:05:35 2020 +0000
+++ b/flye.xml	Sun Aug 22 14:17:05 2021 +0000
@@ -70,8 +70,9 @@
      ]]>            </help>
         </param>
         <param name="mode" type="select" label="Mode">
-            <option value="--nano-raw">Nanopore raw</option>
-            <option value="--nano-corr">Nanopore corrected</option>
+            <option value="--nano-raw">ONT regular reads, pre-Guppy5</option>
+            <option value="--nano-corr">ONT reads that were corrected with other methods</option>
+            <option value="--nano-hq">ONT high-quality reads Guppy5+ or Q20</option>
             <option value="--pacbio-raw">PacBio raw</option>
             <option value="--pacbio-corr">PacBio corrected</option>
             <option value="--subassemblies">high-quality contig-like input</option>
@@ -100,7 +101,7 @@
         <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
         <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" help="This sets a minimum overlap length for two reads to be considered overlapping. In the latest Flye versions, this parameter is chosen automatically based on the read length distribution (reads N90) and does not require manual setting. Typical value is 3k-5k (and down to 1k for datasets with shorter read length). Intuitively, we want to set this parameter as high as possible, so the repeat graph is less tangled. However, higher values might lead to assembly gaps. In some rare cases (for example in case of biased read length distribution) it makes sense to set this parameter manualy."/>
         <param argument="--asm_coverage" type="integer" optional="true" label="reduced coverage for initial contig assembly (default: not set)" />
-        <param argument="--plasmid" type="boolean" truevalue="--plasmid" falsevalue="" checked="False" label="rescue short unassmebled plasmids" />
+        <param argument="--plasmid" type="boolean" truevalue="--plasmid" falsevalue="" checked="False" label="rescue short unassmebled plasmids" help = "Deprecated since version 2.9"/>
         <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="metagenome / uneven coverage mode" />
         <param argument="--no_trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip Trestle stage" help="After resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies"/>
     </inputs>
diff -r 13ed2ccb0fb2 -r 931aefbda8d5 macros.xml
--- a/macros.xml	Thu Aug 06 14:05:35 2020 +0000
+++ b/macros.xml	Sun Aug 22 14:17:05 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.8</token>
+    <token name="@VERSION@">2.9</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@VERSION@">flye</requirement>