# HG changeset patch
# User iuc
# Date 1506504694 14400
# Node ID 269da71211fff2b07a3b29c958fec4dedb114738
# Parent  02a822e32de717f4adc92310333165fb83e56c98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit a548ae243797050890b7b65cdcced2799f098623

diff -r 02a822e32de7 -r 269da71211ff megahit_wrapper.xml
--- a/megahit_wrapper.xml	Sun Sep 24 10:40:12 2017 -0400
+++ b/megahit_wrapper.xml	Wed Sep 27 05:31:34 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool id="megahit" name="MEGAHIT" version="1.1.2">
+<tool id="megahit" name="MEGAHIT" version="1.1.2.1">
     <description>metagenomics assembly</description>
     <requirements>
         <requirement type="package" version="1.1.2">megahit</requirement>
@@ -28,6 +28,7 @@
     --bubble-level '${advanced_section.bubble_level}'
     --merge-level '${advanced_section.merge_level}'
     --prune-level '${advanced_section.prune_level}'
+    --prune-depth '${advanced_section.prune_depth}'
     --low-local-ratio '${advanced_section.low_local_ratio}'
     ${advanced_section.nolocal}
     ${advanced_section.kmin1pass}
@@ -54,15 +55,16 @@
         <section name="basic_section" title="Basic assembly options" expanded="True">
             <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
             <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
-            <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="127" help="must be odd number"/>
-            <param name="k_max" argument="--k-max" type="integer" value="99" label="maximum kmer size" max="127" help="must be odd number"/>
-            <param name="k_step" argument="--k-step" type="integer" value="20" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
+            <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>
+            <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
+            <param name="k_step" argument="--k-step" type="integer" value="12" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
         </section>
         <section name="advanced_section" title="Advanced assembly options" expanded="False">
             <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue=""  label="do not add mercy kmers" />
-            <param name="bubble_level" argument="--bubble-level" type="integer" value="0" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" />
-            <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles" value="20,0.98" />
-            <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="2" label="strength of local low depth pruning" />
+            <param name="bubble_level" argument="--bubble-level" type="integer" value="2" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" />
+            <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
+            <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
+            <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" />
             <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" />
             <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
             <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />
diff -r 02a822e32de7 -r 269da71211ff test-data/paired_result.fa
--- a/test-data/paired_result.fa	Sun Sep 24 10:40:12 2017 -0400
+++ b/test-data/paired_result.fa	Wed Sep 27 05:31:34 2017 -0400
@@ -1,2 +1,2 @@
->k99_1 flag=1 multi=111.0000 len=390
+>k141_1 flag=1 multi=107.0000 len=390
 CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG