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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit b537a57a1de919afa1c6a23048862676b87d7c18"
author pimarin
date Tue, 24 May 2022 06:35:06 +0000
parents 512dc05a0e5a
children
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.8.1</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
2
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
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5 <token name="@PROFILE@">21.05</token>
0
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6 <xml name="version_command">
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7 <version_command><![CDATA[rcf -V]]></version_command>
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8 </xml>
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9 <xml name="xrefs">
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10 <xrefs>
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11 <xref type='bio.tools'>Recentrifuge</xref>
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12 </xrefs>
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13 </xml>
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14 <xml name="requirements">
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">recentrifuge</requirement>
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17 </requirements>
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18 </xml>
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19 <xml name="input_database">
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20 <section name="database" title="Database type" expanded="true">
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21 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
4
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22 <options from_data_table="recentrifuge_database">
0
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23 <validator message="No recentrifuge database is available" type="no_options" />
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24 </options>
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25 </param>
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26 </section>
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27 </xml>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
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28 <xml name="citations">
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29 <citations>
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30 <citation type="bibtex">
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31 @article{10.1371/journal.pcbi.1006967,
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32 doi = {10.1371/journal.pcbi.1006967},
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33 author = {Martí, Jose Manuel},
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34 journal = {PLOS Computational Biology},
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35 publisher = {Public Library of Science},
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36 title = {Recentrifuge: Robust comparative analysis and contamination removal for metagenomics},
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37 year = {2019},
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38 month = {04},
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39 volume = {15},
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40 url = {https://doi.org/10.1371/journal.pcbi.1006967},
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41 pages = {1-24},
4
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42 abstract = {Metagenomic sequencing is becoming widespread in biomedical and environmental research,
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43 and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample,
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44 the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory,
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45 and host related contaminants complicate such analysis.
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46 Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all.
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47 Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples.
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48 With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts
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49 with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples,
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50 Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis
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51 in environmental and clinical metagenomics. Regarding the first area,
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52 Recentrifuge’s novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display
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53 similar taxonomic profiles.
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54 In the clinical field, to confirm Recentrifuge’s ability to analyze complex metagenomes,
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55 we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical
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56 contamination to the point of preventing any positive conclusion.
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57 Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a
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58 blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract.
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59 We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm,
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60 which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants.
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61 Recentrifuge’s official website is www.recentrifuge.org.
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62 The data and source code are anonymously and freely available on GitHub and PyPI.
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63 The computing code is licensed under the AGPLv3.
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64 The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge,
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65 covering installation, use cases, testing, and other useful topics.},
0
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66 number = {4},
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67 }
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68 </citation>
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69 </citations>
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70 </xml>
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71 </macros>