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annotate megahit_wrapper.xml @ 2:331e25f95bf5 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 08:10:23 -0500
parents 9ec09d997274
children 7ec0eb46cc42
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fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="megahit" name="MEGAHIT" version="@VERSION@.2">
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3 <description>for metagenomics assembly</description>
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4 <macros>
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5 <token name="@VERSION@">1.1.2</token>
331e25f95bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 253c8001abdb4530aeca8c79eb25103d0e422f9c
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">megahit</requirement>
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9 </requirements>
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10 <version_command>megahit --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 megahit
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13 #if $input_option.choice == 'paired'
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14 -1 '${input_option.fastq_input1}'
331e25f95bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 253c8001abdb4530aeca8c79eb25103d0e422f9c
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15 -2 '${input_option.fastq_input2}'
331e25f95bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 253c8001abdb4530aeca8c79eb25103d0e422f9c
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16 #else if $input_option.choice == 'paired_collection'
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17 -1 ${ ','.join(['"%s"' % x.forward for x in $input_option.fastq_input1]) }
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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18 -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) }
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19 #else
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20 -r '${input_option.single_files}'
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21 #end if
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22 ##basic assembly
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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23 --min-count '${basic_section.min_count}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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24 --k-min '${basic_section.k_min}'
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25 --k-max '${basic_section.k_max}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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26 --k-step '${basic_section.k_step}'
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27 --min-contig-len '${basic_section.min_contig_len}'
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28 ##advanced assembly
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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29 ${advanced_section.nomercy}
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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30 --bubble-level '${advanced_section.bubble_level}'
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31 --merge-level '${advanced_section.merge_level}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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32 --prune-level '${advanced_section.prune_level}'
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33 --prune-depth '${advanced_section.prune_depth}'
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34 --low-local-ratio '${advanced_section.low_local_ratio}'
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35 ${advanced_section.nolocal}
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36 ${advanced_section.kmin1pass}
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37 && cat megahit_out/log
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38 ]]></command>
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39 <inputs>
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40 <conditional name="input_option">
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41 <param name="choice" type="select" label="Select your input option">
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42 <option value="single" selected="true">Single</option>
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43 <option value="paired">Paired-end</option>
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44 <option value="paired_collection">Paired-end collection</option>
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45 </param>
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46 <when value="single">
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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" />
331e25f95bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 253c8001abdb4530aeca8c79eb25103d0e422f9c
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48 </when>
0
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49 <when value="paired">
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50 <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>
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51 <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/>
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52 </when>
2
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53 <when value="paired_collection">
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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"/>
0
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55 </when>
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56 </conditional>
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57 <section name="basic_section" title="Basic assembly options" expanded="True">
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58 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
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59 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
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60 <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>
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61 <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
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62 <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"/>
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63 </section>
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64 <section name="advanced_section" title="Advanced assembly options" expanded="False">
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65 <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue="" label="do not add mercy kmers" />
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66 <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" />
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67 <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
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68 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
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69 <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" />
0
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70 <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" />
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71 <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
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72 <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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73 </section>
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74 </inputs>
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75 <outputs>
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76 <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
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77 </outputs>
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78 <tests>
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79 <test>
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80 <conditional name="input_option">
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81 <param name="choice" value="single"/>
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82 <param name="single_files" value="refExample.fa" ftype="fasta"/>
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83 </conditional>
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84 <output name="output" file="single_result.fa"/>
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85 </test>
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86 <test>
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87 <conditional name="input_option">
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88 <param name="choice" value="paired"/>
2
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89 <param name="fastq_input1" value="paired-fq1.fa"/>
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90 <param name="fastq_input2" value="paired-fq2.fa"/>
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91 </conditional>
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92 <output name="output" file="paired_result.fa"/>
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93 </test>
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94 <test>
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95 <conditional name="input_option">
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96 <param name="choice" value="paired_collection"/>
0
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97 <param name="fastq_input1">
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98 <collection type="list:paired">
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99 <element name="Pair1">
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100 <collection type="paired">
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101 <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
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102 <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
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103 </collection>
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104 </element>
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105 </collection>
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106 </param>
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107 </conditional>
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108 <output name="output" file="paired_result.fa"/>
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109 </test>
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110 </tests>
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111 <help><![CDATA[
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112
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113 **What it does**
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114
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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.
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116
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117 --------
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118
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119 **Project links:**
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120
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121 https://github.com/voutcn/megahit
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122
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123
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124 ]]></help>
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125 <citations>
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126 <citation type="doi">10.1093/bioinformatics/btv033</citation>
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127 </citations>
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128 </tool>