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1 <tool id="commet" name="commet" version="24.7.14">
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2 <description>COmpare Multiple METagenomes</description>
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3 <requirements>
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4 <requirement type="package" version="24.7.14">commet</requirement>
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4
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5 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 commet.py
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3
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9 #for $set in $sets
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10 --set ${set.setname}::${set.reads}
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11 #end for
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12 -k $kmer
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13 -t $minsharedkmer
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14 -l $minlengthread
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15 -e $minshannonindex
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16 #if str( $options_advanced.options_advanced_selector ) == "advanced"
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17 -m $options_advanced.maxreads
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18 -n $options_advanced.maxn
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19 #end if
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20 --output $output
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21 --output_vectors $output_vectors
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22 --output_dendro $output_dendro
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23 --output_matrix $output_matrix
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24 --output_heatmap1 $output_heatmap1
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25 --output_heatmap2 $output_heatmap2
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26 --output_heatmap3 $output_heatmap3
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27 </command>
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28
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29 <inputs>
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30 <!-- Input data files -->
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3
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31 <repeat name="sets" title="Read sets" min="1">
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32 <param name="reads" type="data" multiple="true" format="fasta, fastq, fastq.gz" label="Dataset" help="Accept fasta/fastq/fastq.gz"/>
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33 <param name="setname" type="text" label="Set name" value="set_name" help="Please don't use spaces or special characters"/>
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34 </repeat>
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35 <param name="kmer" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
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36 <param name="minsharedkmer" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
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37 <param name="minlengthread" type="integer" label="Read mini length" value="0" help="Minimal length a read should have to be kept." />
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38 <param name="minshannonindex" type="float" label="Mini Shannon index" value="0" help="Minimal Shannon index a read should have to be kept. Float in [0,2.32]" />
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39 <conditional name="options_advanced">
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40 <param name="options_advanced_selector" type="select" label="Reads filter options" help="by default, all reads are kept with no Ns limitation">
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41 <option value="default" selected="true">default</option>
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42 <option value="advanced">advanced</option>
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43 </param>
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44 <when value="advanced">
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45 <param name="maxreads" type="integer" value="600" label="Maximum number of selected reads in sets" help="Maximum number of selected reads in sets. If a set is composed by 3 read files, and this option = 600, then the first 200 reads from each read file will be treated" />
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46 <param name="maxn" type="integer" value="5" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept." />
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data format="zip" name="output_vectors" label="${tool.name} on ${on_string}: vector.zip" />
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52 <data format="zip" name="output_logs" label="${tool.name} on ${on_string}: logs.zip" />
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53 <data format="png" name="output_dendro" label="${tool.name} on ${on_string}: dendrogram.png" />
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54 <data format="zip" name="output_matrix" label="${tool.name} on ${on_string}: matrix.zip" />
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55 <data format="png" name="output_heatmap1" label="${tool.name} on ${on_string}: heatmap_normalized.png" />
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56 <data format="png" name="output_heatmap2" label="${tool.name} on ${on_string}: heatmap_percentage.png" />
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57 <data format="png" name="output_heatmap3" label="${tool.name} on ${on_string}: heatmap_plain.png" />
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58 </outputs>
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3
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59 <stdio>
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60 <exit_code range="1" level="fatal" description="Error in Commet execution" />
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61 </stdio>
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62 <help>
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63
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64 **Description**
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65
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66 COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.
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67
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68 Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation of read files, that can be used to further combine read subsets by common logical operations. Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps.
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69
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70
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71 -------
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72
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73 **Web site**
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74
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75 http://colibread.inria.fr/commet/
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76
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77 -------
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78
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79 **Integrated by**
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80
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81 Yvan Le Bras and Cyril Monjeaud
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82
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83 GenOuest Bio-informatics Core Facility
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84
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85 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
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86
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87 support@genouest.org
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88
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89 If you use this tool in Galaxy, please cite :
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90
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91 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_
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92
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93
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94 </help>
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95 <citations>
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96 <citation type="doi">10.1186/1471-2105-13-S19-S10</citation>
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97 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
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98 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
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99 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
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100 booktitle = {JOBIM 2013 Proceedings},
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101 year = {2013},
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102 url = {https://www.e-biogenouest.org/resources/128},
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103 pages = {97-106}
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104 }
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105 </citation>
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106 </citations>
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107
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108 </tool>
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109
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