# HG changeset patch
# User iuc
# Date 1641747464 0
# Node ID 14ddfc8ffb9353a6a6d2756b687cde3e2bfaf6a0
# Parent  7518ee87b53d04113c79321bc53eafcc4c70bc8b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit f311029d3c60675994e8f1a341bf2968a2ed9c10"

diff -r 7518ee87b53d -r 14ddfc8ffb93 megahit_wrapper.xml
--- a/megahit_wrapper.xml	Tue Sep 08 08:34:21 2020 +0000
+++ b/megahit_wrapper.xml	Sun Jan 09 16:57:44 2022 +0000
@@ -1,11 +1,14 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool id="megahit" name="MEGAHIT" version="@VERSION@.5">
+<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy0">
     <description>for metagenomics assembly</description>
+    <xrefs>
+        <xref type="bio.tools">megahit</xref>
+    </xrefs>
     <macros>
-        <token name="@VERSION@">1.1.3</token>
+        <token name="@TOOL_VERSION@">1.2.9</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@VERSION@">megahit</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">megahit</requirement>
     </requirements>
     <version_command>megahit --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -43,7 +46,9 @@
     --merge-level '${advanced_section.merge_level}'
     --prune-level '${advanced_section.prune_level}'
     --prune-depth '${advanced_section.prune_depth}'
+	--disconnect-ratio '${advanced_section.disconnect_ratio}'
     --low-local-ratio '${advanced_section.low_local_ratio}'
+	--cleaning-rounds '${advanced_section.cleaning_rounds}'					  
     ${advanced_section.nolocal}
     ${advanced_section.kmin1pass}
     --min-contig-len '${output_section.min_contig_len}'
@@ -90,27 +95,29 @@
                     <option value="klim_method">Specify min, max, and step values</option>
                 </param>
                 <when value="klist_method">
-                    <param name="k_list" argument="--k-list" type="text" value="21,29,39,59,79,99,119,141" label="comma-separated list of kmer size" help="all must be odd, in the range 15-255, and with increments &lt;= 28"/>
+                    <param name="k_list" argument="--k-list" type="text" value="21,29,39,59,79,99,119,141" label="Comma-separated list of kmer size" help="all must be odd, in the range 15-255, and with increments &lt;= 28"/>
                 </when>
                 <when value="klim_method"> 
-                    <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size." max="255" help="Must be odd number. For ultra complex metagenomics data such as soil, a larger kmin, say 27, is recommended to reduce the complexity of the de Bruijn graph. Quality trimming is also recommended. For high-depth generic data, large --k-min (25 to 31) is recommended. Smaller --k-step, say 10, is more friendly to low-coverage datasets."/>
-                    <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"/>
+                    <param name="k_min" argument="--k-min" type="integer" value="21" label="Minimum kmer size" max="255" help="Must be odd number. For ultra complex metagenomics data such as soil, a larger kmin, say 27, is recommended to reduce the complexity of the de Bruijn graph. Quality trimming is also recommended. For high-depth generic data, large --k-min (25 to 31) is recommended. Smaller --k-step, say 10, is more friendly to low-coverage datasets."/>
+                    <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"/>
                 </when>
             </conditional>
         </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" help="Mercy kmers are specially designed for metagenomics assembly to recover low coverage sequences. For generic dataset >= 30x, MEGAHIT may generate better results with no mercy kmers." />
-            <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" />
+            <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue="" label="Do not add mercy kmers" help="Mercy kmers are specially designed for metagenomics assembly to recover low coverage sequences. For generic dataset >= 30x, MEGAHIT may generate better results with no mercy kmers." />
+            <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" value="20,0.95" label="Merge complex bubbles of length" />
+            <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="disconnect_ratio" argument="--disconnect-ratio" type="float" value="0.1" label="Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings" />
+            <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="Remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods" />
+			<param name="cleaning_rounds" argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" />	  
+            <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" />
         </section>
         <section name="output_section" title="Output 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_contig_len" argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" />
             <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>
         </section>
     </inputs>
@@ -129,7 +136,7 @@
             </conditional>
             <output name="output">
             <assert_contents>
-              <has_line_matching expression=">k21_1 flag=3 multi=1.0486 len=576" />
+              <has_line_matching expression=">k21_0 flag=3 multi=1.0486 len=576" />
             </assert_contents>
             </output>
         </test>
diff -r 7518ee87b53d -r 14ddfc8ffb93 test-data/interleaved_result.fa
--- a/test-data/interleaved_result.fa	Tue Sep 08 08:34:21 2020 +0000
+++ b/test-data/interleaved_result.fa	Sun Jan 09 16:57:44 2022 +0000
@@ -1,2 +1,2 @@
->k59_1 flag=1 multi=8.7336 len=1215
-TGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCTTCGCCCAGTTCCAGATCCCTTGCCTGATTAAA
+>k59_0 flag=1 multi=7.5929 len=1221
+CTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGAT
diff -r 7518ee87b53d -r 14ddfc8ffb93 test-data/paired_result.fa
--- a/test-data/paired_result.fa	Tue Sep 08 08:34:21 2020 +0000
+++ b/test-data/paired_result.fa	Sun Jan 09 16:57:44 2022 +0000
@@ -1,2 +1,2 @@
->k141_1 flag=1 multi=106.0000 len=390
-CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG
+>k141_0 flag=1 multi=29.0000 len=330
+CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAG