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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit acac4f9e3f82cc7248177b97d1cbabbf58d24cf6
author iuc
date Thu, 13 Feb 2025 19:36:06 +0000
parents d27f770bf397
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7:d27f770bf397 8:e1475fcac99c
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy2">
2 <tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy0">
3 <description>for metagenomics assembly</description> 2 <description>for metagenomics assembly</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.2.9</token>
5 </macros>
4 <xrefs> 6 <xrefs>
5 <xref type="bio.tools">megahit</xref> 7 <xref type="bio.tools">megahit</xref>
6 </xrefs> 8 </xrefs>
7 <macros>
8 <token name="@TOOL_VERSION@">1.2.9</token>
9 </macros>
10 <requirements> 9 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">megahit</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">megahit</requirement>
12 </requirements> 11 </requirements>
13 <version_command>megahit --version</version_command> 12 <version_command>megahit --version</version_command>
14 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 if [[ -n "\$GALAXY_MEMORY_MB" ]]; then
15 MEMORY="-m \$((GALAXY_MEMORY_MB * 1024))";
16 fi;
17
15 megahit 18 megahit
16 --num-cpu-threads \${GALAXY_SLOTS:-4} 19 --num-cpu-threads \${GALAXY_SLOTS:-4}
17 #if $input_option.choice == 'paired' 20 #if $input_option.choice == 'paired'
18 -1 '${input_option.fastq_input1}' 21 -1 '${input_option.fastq_input1}'
19 -2 '${input_option.fastq_input2}' 22 -2 '${input_option.fastq_input2}'
50 --low-local-ratio '${advanced_section.low_local_ratio}' 53 --low-local-ratio '${advanced_section.low_local_ratio}'
51 --cleaning-rounds '${advanced_section.cleaning_rounds}' 54 --cleaning-rounds '${advanced_section.cleaning_rounds}'
52 ${advanced_section.nolocal} 55 ${advanced_section.nolocal}
53 ${advanced_section.kmin1pass} 56 ${advanced_section.kmin1pass}
54 --min-contig-len '${output_section.min_contig_len}' 57 --min-contig-len '${output_section.min_contig_len}'
55 && cat megahit_out/log 58 \$MEMORY
56 ]]></command> 59 ]]></command>
57 <inputs> 60 <inputs>
58 <conditional name="input_option"> 61 <conditional name="input_option">
59 <param name="choice" type="select" label="Select your input option"> 62 <param name="choice" type="select" label="Select your input option">
60 <option value="single" selected="true">Single</option> 63 <option value="single" selected="true">Single</option>
86 </when> 89 </when>
87 </conditional> 90 </conditional>
88 </when> 91 </when>
89 </conditional> 92 </conditional>
90 <section name="basic_section" title="Basic assembly options" expanded="True"> 93 <section name="basic_section" title="Basic assembly options" expanded="True">
91 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers" help="(kmin+1)-mer with multiplicity lower than d (default 2, specified by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assemblies, please change this value according to the sequencing depth. (recommend --min-count 3 for >40x)."/> 94 <param argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers" help="(kmin+1)-mer with multiplicity lower than d (default 2, specified by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assemblies, please change this value according to the sequencing depth. (recommend --min-count 3 for >40x)."/>
92 <conditional name="k_mer"> 95 <conditional name="k_mer">
93 <param name="k_mer_method" type="select" label="K-mer specification method"> 96 <param name="k_mer_method" type="select" label="K-mer specification method">
94 <option value="klist_method">Specify list</option> 97 <option value="klist_method">Specify list</option>
95 <option value="klim_method">Specify min, max, and step values</option> 98 <option value="klim_method">Specify min, max, and step values</option>
96 </param> 99 </param>
97 <when value="klist_method"> 100 <when value="klist_method">
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"/> 101 <param 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"/>
99 </when> 102 </when>
100 <when value="klim_method"> 103 <when value="klim_method">
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."/> 104 <param 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."/>
102 <param name="k_max" argument="--k-max" type="integer" value="141" label="Maximum kmer size" max="255" help="must be odd number"/> 105 <param argument="--k-max" type="integer" value="141" label="Maximum kmer size" max="255" help="must be odd 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"/> 106 <param argument="--k-step" type="integer" value="12" label="Increment of kmer size of each iteration" max="28" help="must be even number"/>
104 </when> 107 </when>
105 </conditional> 108 </conditional>
106 </section> 109 </section>
107 <section name="advanced_section" title="Advanced assembly options" expanded="False"> 110 <section name="advanced_section" title="Advanced assembly options" expanded="False">
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." /> 111 <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." />
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" /> 112 <param argument="--bubble-level" type="integer" value="2" min="0" max="2" label="Intensity of bubble merging (0-2), 0 to disable" />
110 <param name="merge_level" argument="--merge-level" type="text" value="20,0.95" label="Merge complex bubbles of length" /> 113 <param argument="--merge-level" type="text" value="20,0.95" label="Merge complex bubbles of length" />
111 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="Strength of low depth pruning" /> 114 <param argument="--prune-level" type="integer" value="2" min="0" max="3" label="Strength of low depth pruning" />
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" /> 115 <param argument="--prune-depth" type="integer" value="2" min="0" label="Remove unitigs with avg kmer depth less than this value" />
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" /> 116 <param 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" />
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" /> 117 <param 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" />
115 <param name="cleaning_rounds" argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" /> 118 <param 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" /> 119 <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" /> 120 <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="Use 1pass mode to build SdBG of k_min" />
118 </section> 121 </section>
119 <section name="output_section" title="Output options" expanded="True"> 122 <section name="output_section" title="Output options" expanded="True">
120 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" /> 123 <param argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" />
121 <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/> 124 <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>
125 <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/>
122 </section> 126 </section>
123 </inputs> 127 </inputs>
124 <outputs> 128 <outputs>
125 <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" /> 129 <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
126 <collection name="intermediate_contigs" type="list" label="Intermediate contigs from ${tool.name} on ${on_string}"> 130 <collection name="intermediate_contigs" type="list" label="Intermediate contigs from ${tool.name} on ${on_string}">
127 <filter>output_section['show_intermediate_contigs']</filter> 131 <filter>output_section['show_intermediate_contigs']</filter>
128 <discover_datasets pattern="(?P&lt;designation&gt;.*\d)\.contigs\.fa$" ext="fasta" directory="megahit_out/intermediate_contigs" /> 132 <discover_datasets pattern="(?P&lt;designation&gt;.*\d)\.contigs\.fa$" ext="fasta" directory="megahit_out/intermediate_contigs" />
129 </collection> 133 </collection>
134 <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)" from_work_dir="megahit_out/log">
135 <filter>output_section['log_file']</filter>
136 </data>
130 </outputs> 137 </outputs>
131 <tests> 138 <tests>
132 <test> 139 <test expect_num_outputs="2">
133 <conditional name="input_option"> 140 <conditional name="input_option">
134 <param name="choice" value="single"/> 141 <param name="choice" value="single"/>
135 <param name="single_files" value="refExample.fa" ftype="fasta"/> 142 <param name="single_files" value="refExample.fa" ftype="fasta"/>
136 </conditional> 143 </conditional>
144 <param name="log_file" value="true"/>
137 <output name="output"> 145 <output name="output">
138 <assert_contents> 146 <assert_contents>
139 <has_line_matching expression=">k21_0 flag=3 multi=1.0486 len=576" /> 147 <has_line_matching expression=">k21_0 flag=3 multi=1.0505 len=576" />
140 </assert_contents> 148 </assert_contents>
141 </output> 149 </output>
142 </test> 150 <output name="log_output">
143 <test> 151 <assert_contents>
152 <has_text text="- MEGAHIT v"/>
153 <has_text text="- Build graph for k = 21"/>
154 <has_text text="- Assemble contigs from SdBG for k = 21"/>
155 <has_text text="- Local assembly for k = 21"/>
156 </assert_contents>
157 </output>
158 </test>
159 <test expect_num_outputs="1">
144 <conditional name="input_option"> 160 <conditional name="input_option">
145 <param name="choice" value="interleaved"/> 161 <param name="choice" value="interleaved"/>
146 <param name="interleaved_file" value="interleaved-fq.fa"/> 162 <param name="interleaved_file" value="interleaved-fq.fa"/>
147 </conditional> 163 </conditional>
148 <output name="output" file="interleaved_result.fa"/> 164 <output name="output" file="interleaved_result.fa"/>
149 </test> 165 </test>
150 <test> 166 <test expect_num_outputs="1">
151 <conditional name="input_option"> 167 <conditional name="input_option">
152 <param name="choice" value="paired"/> 168 <param name="choice" value="paired"/>
153 <param name="fastq_input1" value="paired-fq1.fa"/> 169 <param name="fastq_input1" value="paired-fq1.fa"/>
154 <param name="fastq_input2" value="paired-fq2.fa"/> 170 <param name="fastq_input2" value="paired-fq2.fa"/>
155 </conditional> 171 </conditional>
156 <output name="output" file="paired_result.fa"/> 172 <output name="output" file="paired_result.fa"/>
157 </test> 173 </test>
158 <test> 174 <test expect_num_outputs="1">
159 <conditional name="input_option"> 175 <conditional name="input_option">
160 <param name="choice" value="paired_collection"/> 176 <param name="choice" value="paired_collection"/>
161 <conditional name="batchmode"> 177 <conditional name="batchmode">
162 <param name="processmode" value="merge"/> 178 <param name="processmode" value="merge"/>
163 <param name="pair_input_list"> 179 <param name="pair_input_list">