Merge pull request #1491 from cmonjeau/fix-megahit-default-values

Fix megahit default values

tools/megahit/megahit_wrapper.xml

@@ -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" />

tools/megahit/test-data/paired_result.fa

@@ -1,2 +1,2 @@
->k99_1 flag=1 multi=111.0000 len=390
+>k141_1 flag=1 multi=107.0000 len=390
 CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG