| Previous changeset 0:02a822e32de7 (2017-09-24) Next changeset 2:edc663aadfa8 (2017-11-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit a548ae243797050890b7b65cdcced2799f098623 |
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modified:
megahit_wrapper.xml test-data/paired_result.fa |
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| 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 |
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| @@ -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" /> |
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| 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 |
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| @@ -1,2 +1,2 @@ ->k99_1 flag=1 multi=111.0000 len=390 +>k141_1 flag=1 multi=107.0000 len=390 CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG |