Mercurial > repos > iuc > megahit

annotate megahit_wrapper.xml @ 0:fc282b8cf3b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
author iuc
date Sun, 24 Sep 2017 10:39:54 -0400
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children 9ec09d997274
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fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
iuc
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1 <?xml version='1.0' encoding='utf-8'?>
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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2 <tool id="megahit" name="MEGAHIT" version="1.1.2">
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3 <description>metagenomics assembly</description>
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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4 <requirements>
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5 <requirement type="package" version="1.1.2">megahit</requirement>
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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6 </requirements>
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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7 <version_command>megahit --version</version_command>
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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8 <command detect_errors="exit_code"><![CDATA[
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9
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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10 megahit
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11
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12 #if $input_option.choice == 'paired'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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13 -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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14 -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.fastq_input1]) }
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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15 #else
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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16 -r '${input_option.single_files}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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17 #end if
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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18
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19 ##basic assembly
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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20 --min-count '${basic_section.min_count}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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21 --k-min '${basic_section.k_min}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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22 --k-max '${basic_section.k_max}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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23 --k-step '${basic_section.k_step}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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24 --min-contig-len '${basic_section.min_contig_len}'
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25
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26 ##advanced assembly
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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27 ${advanced_section.nomercy}
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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28 --bubble-level '${advanced_section.bubble_level}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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29 --merge-level '${advanced_section.merge_level}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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30 --prune-level '${advanced_section.prune_level}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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31 --low-local-ratio '${advanced_section.low_local_ratio}'
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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32 ${advanced_section.nolocal}
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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33 ${advanced_section.kmin1pass}
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34
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35 &&
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36
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37 cat megahit_out/log
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38
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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39 ]]></command>
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40
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41 <inputs>
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42 <conditional name="input_option">
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43 <param name="choice" type="select" label="Select your input option">
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44 <option value="single" selected="true">Single</option>
fc282b8cf3b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 7da69f4b449643fd80cfb824251642b4e8638b44
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45 <option value="paired">Paired-end</option>
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46 </param>
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47 <when value="paired">
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48 <param name="fastq_input1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="list:paired" label="Select a paired collection"/>
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49 </when>
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50 <when value="single">
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51 <param name="single_files" multiple="true" format="fastq,fastqsanger,fasta" type="data" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />
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52 </when>
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53 </conditional>
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54 <section name="basic_section" title="Basic assembly options" expanded="True">
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55 <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
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56 <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
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57 <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="127" help="must be odd number"/>
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58 <param name="k_max" argument="--k-max" type="integer" value="99" label="maximum kmer size" max="127" help="must be odd number"/>
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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"/>
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60 </section>
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61 <section name="advanced_section" title="Advanced assembly options" expanded="False">
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62 <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue="" label="do not add mercy kmers" />
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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" />
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64 <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles" value="20,0.98" />
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65 <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="2" label="strength of local low depth pruning" />
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66 <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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67 <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
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68 <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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69 </section>
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70 </inputs>
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71 <outputs>
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72 <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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73 </outputs>
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74 <tests>
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75 <test>
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76 <conditional name="input_option">
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77 <param name="choice" value="single"/>
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78 <param name="single_files" value="refExample.fa" ftype="fasta"/>
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79 </conditional>
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80 <output name="output" file="single_result.fa"/>
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81 </test>
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82 <test>
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83 <conditional name="input_option">
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84 <param name="choice" value="paired"/>
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85 <param name="fastq_input1">
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86 <collection type="list:paired">
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87 <element name="Pair1">
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88 <collection type="paired">
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89 <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
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90 <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
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91 </collection>
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92 </element>
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93 </collection>
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94 </param>
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95 </conditional>
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96 <output name="output" file="paired_result.fa"/>
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97 </test>
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98 </tests>
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99
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100 <help><![CDATA[
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101
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102 **What it does**
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103
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104 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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105
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106 --------
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107
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108 **Project links:**
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109
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110 https://github.com/voutcn/megahit
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111
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112
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113 ]]></help>
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114 <citations>
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115 <citation type="doi">10.1093/bioinformatics/btv033</citation>
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116 </citations>
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117 </tool>