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1 <tool id="metaphlan" name="MetaPhlAn" version="1.0">
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2 <requirements>
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3 <requirement type="package">metaphlan</requirement>
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4 <requirement type="package" version="2.2.25+">blast</requirement>
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5 </requirements>
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6 <description>Metagenomic Phylogenetic Analysis</description>
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7 <command>
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8 metaphlan.py
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9 #if str($source.type) == "fasta":
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10 ${source.fasta_input}
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11 #else:
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12 ${source.blast_input}
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13 #end if
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14 ${metaphlan_out}
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15 --nproc 4
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16 #if str($source.type) == "fasta":
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17 --blastout metagenome.outfmt6.txt
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18 --evalue ${source.evalue}
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19 #end if
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20 --lib_dir ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan
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21 --min_cu_len ${min_cu_len}
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22 --min_nreads ${min_nreads}
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23 </command>
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24 <inputs>
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25
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26 <conditional name="source">
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27 <param name="type" type="select" label="Input Type">
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28 <option value="fasta">multi-fasta file containing metagenomic reads</option>
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29 <option value="blast">NCBI BLAST output file</option>
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30 </param>
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31 <when value="fasta">
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32 <param format="fasta" name="fasta_input" type="data" label="from"/>
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33 <param name="evalue" type="float" size="15" value="0.00001" label="evalue threshold for the blasting" />
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34 </when>
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35 <when value="blast">
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36 <param format="tabular" name="blast_input" type="data" label="from"/>
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37 </when>
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38 </conditional>
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39
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40 <param name="tax_lev" type="select" label="Taxonomic Level" help="The taxonomic level for the relative abundance output">
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41 <option value="a">All taxonomic levels</option>
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42 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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43 <option value="p">Phyla only</option>
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44 <option value="c">Classes only</option>
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45 <option value="o">Orders only</option>
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46 <option value="f">Families only</option>
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47 <option value="g">Genera only</option>
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48 <option value="s">Species only</option>
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49 </param>
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50 <param name="min_cu_len" type="integer" value="10000" help="min_cu_len" label="Minimum total nucleotide length for the unique markers for estimating the abundance without considering children clade abundances" />
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51 <param name="min_nreads" type="integer" value="5" help="min_nreads" label="minimum total reads assigned to a clade for estimating the abundance without considering children clade abundances" />
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52 </inputs>
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53 <outputs>
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54 <data format="tabular" name="metaphlan_out" label="MetaPhlAn on ${on_string}" />
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55 <data format="tabular" name="blast_out" from_work_dir="metagenome.outfmt6.txt" label="MetaPhlAn BLAST on ${on_string}">
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56 <filter>source['type'] == "fasta"</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 </tests>
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61 <help>
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62
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63 **What it does**
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64 MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from reference genomes, allowing orders of magnitude speedups and unambiguous taxonomic assignments.
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65
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66 MetaPhlAn main features are:
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67
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68 More than 100x computational speedup compared to Blast-based approaches or other available methods with species level resolution
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69 Higher accuracy in estimating the true composition of microbial communities in terms of organismal relative abundance
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70 Unambiguous read-to-taxa assignments as conserved inter-clade sequences are removed from the reference sequence data
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71
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72 ---------
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73
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74 **Inputs**
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75
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76 The input file can be a multi-fasta file containing metagenomic reads OR a NCBI BLAST output file (-outfmt 6 format) of the metagenomic read fasta file against the metaflan database.
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77
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78 **outputs**
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79
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80 The output is a tab-separated output file of the predicted taxon relative abundances.
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81 If the input is a multi-fasta file then the output from the BLAST operation is also provided as an additional output.
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82
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83 ---------
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84
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85 **Settings**::
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86
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87 --tax_lev TAXONOMIC_LEVEL
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88 The taxonomic level for the relative abundance
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89 output:
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90 'a' : all taxonomic levels
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91 'k' : kingdoms (Bacteria and Archaea) only
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92 'p' : phyla only
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93 'c' : classes only
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94 'o' : orders only
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95 'f' : families only
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96 'g' : genera only
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97 's' : species only
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98 [default 'a']
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99 --evalue evalue threshold for the blasting
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100 [default 1e-6]
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101 --min_cu_len minimum total nucleotide lenght for the unique
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102 markers for estimating the abundance without
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103 considering children clade abundances
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104 [default 10000]
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105 --min_nreads minimum total reads assigned to a clade for
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106 estimating the abundance without considering
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107 children clade abundances
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108 [default 5]
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109
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110 -----
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111
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112 **Citation**
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113
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114 If you find MetaPhlAn useful in your research, please cite our paper:
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115 Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower.
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116 "Fast and accurate metagenomic profiling of microbial community composition using unique clade-specific marker genes"
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117 ***in review***
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118
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119 </help>
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120 </tool>
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121
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