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author cmonjeau
date Fri, 05 Jun 2015 11:41:26 -0400
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1 <tool id="commet" name="commet" version="24.7.14">
2 <description>COmpare Multiple METagenomes</description>
3 <requirements>
4 <requirement type="package" version="24.7.14">commet</requirement>
5 </requirements>
6 <command interpreter="python">
7 commet.py
8 --input $input
9 -k $kmer
10 -t $minsharedkmer
11 -l $minlengthread
12 -e $minshannonindex
13 #if str( $options_advanced.options_advanced_selector ) == "advanced"
14 -m $options_advanced.maxreads
15 -n $options_advanced.maxn
16 #end if
17 --output $output
18 --output_vectors $output_vectors
19 --output_dendro $output_dendro
20 --output_logs $output_logs
21 --output_matrix $output_matrix
22 --output_heatmap1 $output_heatmap1
23 --output_heatmap2 $output_heatmap2
24 --output_heatmap3 $output_heatmap3
25 </command>
26
27 <inputs>
28 <!-- Input data files -->
29 <param name="input" type="data" format="commet" label="Read sets" help="input read sets a line = a set composed by “set_name: read_file; read_file...“. Generate with Prepare commet tool" />
30 <param name="kmer" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
31 <param name="minsharedkmer" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
32 <param name="minlengthread" type="integer" label="Read mini length" value="0" help="Minimal length a read should have to be kept." />
33 <param name="minshannonindex" type="float" label="Mini Shannon index" value="0" help="Minimal Shannon index a read should have to be kept. Float in [0,2.32]" />
34 <conditional name="options_advanced">
35 <param name="options_advanced_selector" type="select" label="Reads filter options" help="by default, all reads are kept with no Ns limitation">
36 <option value="default" selected="true">default</option>
37 <option value="advanced">advanced</option>
38 </param>
39 <when value="advanced">
40 <param name="maxreads" type="integer" value="600" label="Maximum number of selected reads in sets" help="Maximum number of selected reads in sets. If a set is composed by 3 read files, and this option = 600, then the first 200 reads from each read file will be treated" />
41 <param name="maxn" type="integer" value="5" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept." />
42 </when>
43 </conditional>
44 </inputs>
45
46 <outputs>
47 <data format="txt" name="output" label="${tool.name} on ${on_string}: commet.log" />
48 <data format="zip" name="output_vectors" label="${tool.name} on ${on_string}: vector.zip" />
49 <data format="zip" name="output_logs" label="${tool.name} on ${on_string}: logs.zip" />
50 <data format="png" name="output_dendro" label="${tool.name} on ${on_string}: dendrogram.png" />
51 <data format="zip" name="output_matrix" label="${tool.name} on ${on_string}: matrix.zip" />
52 <data format="png" name="output_heatmap1" label="${tool.name} on ${on_string}: heatmap_normalized.png" />
53 <data format="png" name="output_heatmap2" label="${tool.name} on ${on_string}: heatmap_percentage.png" />
54 <data format="png" name="output_heatmap3" label="${tool.name} on ${on_string}: heatmap_plain.png" />
55 </outputs>
56 <help>
57
58 **Description**
59
60 COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.
61
62 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.
63
64
65 -------
66
67 **Web site**
68
69 http://colibread.inria.fr/commet/
70
71 -------
72
73 **Integrated by**
74
75 Yvan Le Bras and Cyril Monjeaud
76
77 GenOuest Bio-informatics Core Facility
78
79 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
80
81 support@genouest.org
82
83 If you use this tool in Galaxy, please cite :
84
85 `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. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
86
87
88 </help>
89 <citations>
90 <citation type="doi">10.1186/1471-2105-13-S19-S10</citation>
91 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
92 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.},
93 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
94 booktitle = {JOBIM 2013 Proceedings},
95 year = {2013},
96 url = {https://www.e-biogenouest.org/resources/128},
97 pages = {97-106}
98 }
99 </citation>
100 </citations>
101
102 </tool>
103