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comparison megahit_wrapper.xml @ 2:edc663aadfa8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 253c8001abdb4530aeca8c79eb25103d0e422f9c
author iuc
date Fri, 17 Nov 2017 08:10:37 -0500
parents 269da71211ff
children 98242353faa4
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1:269da71211ff 2:edc663aadfa8
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="megahit" name="MEGAHIT" version="1.1.2.1"> 2 <tool id="megahit" name="MEGAHIT" version="@VERSION@.2">
3 <description>metagenomics assembly</description> 3 <description>for metagenomics assembly</description>
4 <macros>
5 <token name="@VERSION@">1.1.2</token>
6 </macros>
4 <requirements> 7 <requirements>
5 <requirement type="package" version="1.1.2">megahit</requirement> 8 <requirement type="package" version="@VERSION@">megahit</requirement>
6 </requirements> 9 </requirements>
7 <version_command>megahit --version</version_command> 10 <version_command>megahit --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
9 12 megahit
10 megahit
11
12 #if $input_option.choice == 'paired' 13 #if $input_option.choice == 'paired'
14 -1 '${input_option.fastq_input1}'
15 -2 '${input_option.fastq_input2}'
16 #else if $input_option.choice == 'paired_collection'
13 -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) } 17 -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) }
14 -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) } 18 -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) }
15 #else 19 #else
16 -r '${input_option.single_files}' 20 -r '${input_option.single_files}'
17 #end if 21 #end if
18
19 ##basic assembly 22 ##basic assembly
20 --min-count '${basic_section.min_count}' 23 --min-count '${basic_section.min_count}'
21 --k-min '${basic_section.k_min}' 24 --k-min '${basic_section.k_min}'
22 --k-max '${basic_section.k_max}' 25 --k-max '${basic_section.k_max}'
23 --k-step '${basic_section.k_step}' 26 --k-step '${basic_section.k_step}'
24 --min-contig-len '${basic_section.min_contig_len}' 27 --min-contig-len '${basic_section.min_contig_len}'
25
26 ##advanced assembly 28 ##advanced assembly
27 ${advanced_section.nomercy} 29 ${advanced_section.nomercy}
28 --bubble-level '${advanced_section.bubble_level}' 30 --bubble-level '${advanced_section.bubble_level}'
29 --merge-level '${advanced_section.merge_level}' 31 --merge-level '${advanced_section.merge_level}'
30 --prune-level '${advanced_section.prune_level}' 32 --prune-level '${advanced_section.prune_level}'
31 --prune-depth '${advanced_section.prune_depth}' 33 --prune-depth '${advanced_section.prune_depth}'
32 --low-local-ratio '${advanced_section.low_local_ratio}' 34 --low-local-ratio '${advanced_section.low_local_ratio}'
33 ${advanced_section.nolocal} 35 ${advanced_section.nolocal}
34 ${advanced_section.kmin1pass} 36 ${advanced_section.kmin1pass}
35 37 && cat megahit_out/log
36 &&
37
38 cat megahit_out/log
39
40 ]]></command> 38 ]]></command>
41
42 <inputs> 39 <inputs>
43 <conditional name="input_option"> 40 <conditional name="input_option">
44 <param name="choice" type="select" label="Select your input option"> 41 <param name="choice" type="select" label="Select your input option">
45 <option value="single" selected="true">Single</option> 42 <option value="single" selected="true">Single</option>
46 <option value="paired">Paired-end</option> 43 <option value="paired">Paired-end</option>
44 <option value="paired_collection">Paired-end collection</option>
47 </param> 45 </param>
46 <when value="single">
47 <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />
48 </when>
48 <when value="paired"> 49 <when value="paired">
49 <param name="fastq_input1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="list:paired" label="Select a paired collection"/> 50 <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>
51 <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/>
50 </when> 52 </when>
51 <when value="single"> 53 <when value="paired_collection">
52 <param name="single_files" multiple="true" format="fastq,fastqsanger,fasta" type="data" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" /> 54 <param name="fastq_input1" type="data_collection" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" collection_type="list:paired" label="Select a paired collection"/>
53 </when> 55 </when>
54 </conditional> 56 </conditional>
55 <section name="basic_section" title="Basic assembly options" expanded="True"> 57 <section name="basic_section" title="Basic assembly options" expanded="True">
56 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" /> 58 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
57 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/> 59 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
82 <output name="output" file="single_result.fa"/> 84 <output name="output" file="single_result.fa"/>
83 </test> 85 </test>
84 <test> 86 <test>
85 <conditional name="input_option"> 87 <conditional name="input_option">
86 <param name="choice" value="paired"/> 88 <param name="choice" value="paired"/>
89 <param name="fastq_input1" value="paired-fq1.fa"/>
90 <param name="fastq_input2" value="paired-fq2.fa"/>
91 </conditional>
92 <output name="output" file="paired_result.fa"/>
93 </test>
94 <test>
95 <conditional name="input_option">
96 <param name="choice" value="paired_collection"/>
87 <param name="fastq_input1"> 97 <param name="fastq_input1">
88 <collection type="list:paired"> 98 <collection type="list:paired">
89 <element name="Pair1"> 99 <element name="Pair1">
90 <collection type="paired"> 100 <collection type="paired">
91 <element name="forward" value="paired-fq1.fa" ftype="fasta"/> 101 <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
96 </param> 106 </param>
97 </conditional> 107 </conditional>
98 <output name="output" file="paired_result.fa"/> 108 <output name="output" file="paired_result.fa"/>
99 </test> 109 </test>
100 </tests> 110 </tests>
101
102 <help><![CDATA[ 111 <help><![CDATA[
103 112
104 **What it does** 113 **What it does**
105 114
106 MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. 115 MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5.