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comparison megahit_wrapper.xml @ 7:d27f770bf397 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit f311029d3c60675994e8f1a341bf2968a2ed9c10"
author iuc
date Sun, 09 Jan 2022 16:57:18 +0000
parents 00f89dc38847
children e1475fcac99c
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6:00f89dc38847 7:d27f770bf397
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="megahit" name="MEGAHIT" version="@VERSION@.5"> 2 <tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy0">
3 <description>for metagenomics assembly</description> 3 <description>for metagenomics assembly</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">megahit</xref> 5 <xref type="bio.tools">megahit</xref>
6 </xrefs> 6 </xrefs>
7 <macros> 7 <macros>
8 <token name="@VERSION@">1.1.3</token> 8 <token name="@TOOL_VERSION@">1.2.9</token>
9 </macros> 9 </macros>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@VERSION@">megahit</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">megahit</requirement>
12 </requirements> 12 </requirements>
13 <version_command>megahit --version</version_command> 13 <version_command>megahit --version</version_command>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 megahit 15 megahit
16 --num-cpu-threads \${GALAXY_SLOTS:-4} 16 --num-cpu-threads \${GALAXY_SLOTS:-4}
44 ${advanced_section.nomercy} 44 ${advanced_section.nomercy}
45 --bubble-level '${advanced_section.bubble_level}' 45 --bubble-level '${advanced_section.bubble_level}'
46 --merge-level '${advanced_section.merge_level}' 46 --merge-level '${advanced_section.merge_level}'
47 --prune-level '${advanced_section.prune_level}' 47 --prune-level '${advanced_section.prune_level}'
48 --prune-depth '${advanced_section.prune_depth}' 48 --prune-depth '${advanced_section.prune_depth}'
49 --disconnect-ratio '${advanced_section.disconnect_ratio}'
49 --low-local-ratio '${advanced_section.low_local_ratio}' 50 --low-local-ratio '${advanced_section.low_local_ratio}'
51 --cleaning-rounds '${advanced_section.cleaning_rounds}'
50 ${advanced_section.nolocal} 52 ${advanced_section.nolocal}
51 ${advanced_section.kmin1pass} 53 ${advanced_section.kmin1pass}
52 --min-contig-len '${output_section.min_contig_len}' 54 --min-contig-len '${output_section.min_contig_len}'
53 && cat megahit_out/log 55 && cat megahit_out/log
54 ]]></command> 56 ]]></command>
91 <param name="k_mer_method" type="select" label="K-mer specification method"> 93 <param name="k_mer_method" type="select" label="K-mer specification method">
92 <option value="klist_method">Specify list</option> 94 <option value="klist_method">Specify list</option>
93 <option value="klim_method">Specify min, max, and step values</option> 95 <option value="klim_method">Specify min, max, and step values</option>
94 </param> 96 </param>
95 <when value="klist_method"> 97 <when value="klist_method">
96 <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"/> 98 <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"/>
97 </when> 99 </when>
98 <when value="klim_method"> 100 <when value="klim_method">
99 <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."/> 101 <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."/>
100 <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/> 102 <param name="k_max" argument="--k-max" type="integer" value="141" label="Maximum kmer size" max="255" help="must be odd number"/>
101 <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"/> 103 <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"/>
102 </when> 104 </when>
103 </conditional> 105 </conditional>
104 </section> 106 </section>
105 <section name="advanced_section" title="Advanced assembly options" expanded="False"> 107 <section name="advanced_section" title="Advanced assembly options" expanded="False">
106 <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." /> 108 <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." />
107 <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" /> 109 <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" />
108 <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" /> 110 <param name="merge_level" argument="--merge-level" type="text" value="20,0.95" label="Merge complex bubbles of length" />
109 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" /> 111 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="Strength of low depth pruning" />
110 <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" /> 112 <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="Remove unitigs with avg kmer depth less than this value" />
111 <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" /> 113 <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" />
112 <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" /> 114 <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" />
113 <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" /> 115 <param name="cleaning_rounds" argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" />
116 <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="Disable local assembly" />
117 <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="Use 1pass mode to build SdBG of k_min" />
114 </section> 118 </section>
115 <section name="output_section" title="Output options" expanded="True"> 119 <section name="output_section" title="Output options" expanded="True">
116 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" /> 120 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" />
117 <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/> 121 <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>
118 </section> 122 </section>
119 </inputs> 123 </inputs>
120 <outputs> 124 <outputs>
121 <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" /> 125 <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
130 <param name="choice" value="single"/> 134 <param name="choice" value="single"/>
131 <param name="single_files" value="refExample.fa" ftype="fasta"/> 135 <param name="single_files" value="refExample.fa" ftype="fasta"/>
132 </conditional> 136 </conditional>
133 <output name="output"> 137 <output name="output">
134 <assert_contents> 138 <assert_contents>
135 <has_line_matching expression=">k21_1 flag=3 multi=1.0486 len=576" /> 139 <has_line_matching expression=">k21_0 flag=3 multi=1.0486 len=576" />
136 </assert_contents> 140 </assert_contents>
137 </output> 141 </output>
138 </test> 142 </test>
139 <test> 143 <test>
140 <conditional name="input_option"> 144 <conditional name="input_option">