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comparison megahit_wrapper.xml @ 1:269da71211ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit a548ae243797050890b7b65cdcced2799f098623
author iuc
date Wed, 27 Sep 2017 05:31:34 -0400
parents 02a822e32de7
children edc663aadfa8
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0:02a822e32de7 1:269da71211ff
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="megahit" name="MEGAHIT" version="1.1.2"> 2 <tool id="megahit" name="MEGAHIT" version="1.1.2.1">
3 <description>metagenomics assembly</description> 3 <description>metagenomics assembly</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1.2">megahit</requirement> 5 <requirement type="package" version="1.1.2">megahit</requirement>
6 </requirements> 6 </requirements>
7 <version_command>megahit --version</version_command> 7 <version_command>megahit --version</version_command>
26 ##advanced assembly 26 ##advanced assembly
27 ${advanced_section.nomercy} 27 ${advanced_section.nomercy}
28 --bubble-level '${advanced_section.bubble_level}' 28 --bubble-level '${advanced_section.bubble_level}'
29 --merge-level '${advanced_section.merge_level}' 29 --merge-level '${advanced_section.merge_level}'
30 --prune-level '${advanced_section.prune_level}' 30 --prune-level '${advanced_section.prune_level}'
31 --prune-depth '${advanced_section.prune_depth}'
31 --low-local-ratio '${advanced_section.low_local_ratio}' 32 --low-local-ratio '${advanced_section.low_local_ratio}'
32 ${advanced_section.nolocal} 33 ${advanced_section.nolocal}
33 ${advanced_section.kmin1pass} 34 ${advanced_section.kmin1pass}
34 35
35 && 36 &&
52 </when> 53 </when>
53 </conditional> 54 </conditional>
54 <section name="basic_section" title="Basic assembly options" expanded="True"> 55 <section name="basic_section" title="Basic assembly options" expanded="True">
55 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" /> 56 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
56 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/> 57 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
57 <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="127" help="must be odd number"/> 58 <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>
58 <param name="k_max" argument="--k-max" type="integer" value="99" label="maximum kmer size" max="127" help="must be odd number"/> 59 <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
59 <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"/> 60 <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"/>
60 </section> 61 </section>
61 <section name="advanced_section" title="Advanced assembly options" expanded="False"> 62 <section name="advanced_section" title="Advanced assembly options" expanded="False">
62 <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue="" label="do not add mercy kmers" /> 63 <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue="" label="do not add mercy kmers" />
63 <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" /> 64 <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" />
64 <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles" value="20,0.98" /> 65 <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
65 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="2" label="strength of local low depth pruning" /> 66 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
67 <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" />
66 <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" /> 68 <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" />
67 <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" /> 69 <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
68 <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" /> 70 <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />
69 </section> 71 </section>
70 </inputs> 72 </inputs>