Mercurial > repos > iuc > colibread_commet

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:55:07 +0000
parents d03353742508
children
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6
4daa32d21ea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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1 <tool id="commet" name="Commet" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
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2 <description>COmpare Multiple METagenomes</description>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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3 <macros>
6
4daa32d21ea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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4 <token name="@TOOL_VERSION@">24.7.14</token>
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5 <import>macros.xml</import>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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6 </macros>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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7 <requirements>
6
4daa32d21ea5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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8 <requirement type="package" version="@TOOL_VERSION@">commet</requirement>
0
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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9 </requirements>
5
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10 <command detect_errors="exit_code"><![CDATA[
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11 #for $i, $set in enumerate($sets):
0
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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12 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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13 #end for
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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14 Commet.py
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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15 -k ${k}
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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16 -t ${t}
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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17 -l ${l}
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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18 -e ${e}
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19 #if str($options_advanced.options_advanced_selector) == "advanced":
0
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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20 -m ${options_advanced.m}
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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21 -n ${options_advanced.n}
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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22 #end if
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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23 commet_input_sets.txt
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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24 ]]></command>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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25 <inputs>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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26 <repeat name="sets" title="Read sets" min="1">
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27 <param name="reads" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="Dataset" help="Accept fasta/fastq"/>
0
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28 </repeat>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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29 <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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30 <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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31 <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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32 <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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33 <conditional name="options_advanced">
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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34 <param name="options_advanced_selector" type="select" label="Reads filter options" help="By default, all reads are kept with no Ns limitation">
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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35 <option value="default" selected="true">default</option>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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36 <option value="advanced">advanced</option>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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37 </param>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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38 <when value="default" />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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39 <when value="advanced">
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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40 <param argument="-m" type="integer" value="-1" 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. (-1 = any)" />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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41 <param argument="-n" type="integer" value="-1" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept. (-1 = all)" />
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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42 </when>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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43 </conditional>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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44 <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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45 <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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46 <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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47 </inputs>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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48 <outputs>
6
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49 <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="${tool.name} on ${on_string}: Matrix plain" >
0
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50 <filter>plain_outputs</filter>
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51 </data>
6
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52 <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="${tool.name} on ${on_string}: Matrix percentage" >
0
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53 <filter>percentage_outputs</filter>
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54 </data>
6
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55 <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="${tool.name} on ${on_string}: Matrix normalized" >
0
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56 <filter>normalized_outputs</filter>
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57 </data>
6
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58 <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="${tool.name} on ${on_string}: Dendrogram" />
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59 <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="${tool.name} on ${on_string}: Heatmap normalized" >
0
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60 <filter>normalized_outputs</filter>
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61 </data>
6
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62 <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="${tool.name} on ${on_string}: Heatmap percentage" >
0
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63 <filter>percentage_outputs</filter>
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64 </data>
6
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65 <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="${tool.name} on ${on_string}: Heatmap Plain" >
0
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66 <filter>plain_outputs</filter>
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67 </data>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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68 </outputs>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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69 <tests>
6
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70 <test expect_num_outputs="5">
0
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71 <repeat name="sets">
5
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72 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
0
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73 </repeat>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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74 <repeat name="sets">
5
d03353742508 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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75 <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" />
0
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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76 </repeat>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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77 <repeat name="sets">
5
d03353742508 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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78 <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" />
0
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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79 </repeat>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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80 <param name="plain_outputs" value="True"/>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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81 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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82 <output name="matrix_plain" file="commet/matrix_plain.csv"/>
6
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83 <output name="heatmap_plain">
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84 <assert_contents>
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85 <has_size size="1k"/>
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86 </assert_contents>
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87 </output>
0
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91
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92 **Description**
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93
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94 COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.
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95
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96 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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97
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98
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99 -------
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100
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101 **Web site**
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102
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103 http://colibread.inria.fr/commet/
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104
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105 ]]></help>
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106 <expand macro="citations">
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107 <citation type="doi">10.1186/1471-2105-13-S19-S10</citation>
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108 </expand>
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109 </tool>