Mercurial > repos > frogs > frogs_2_0_0
annotate filters.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author | frogs |
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date | Thu, 25 Oct 2018 05:01:13 -0400 |
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0
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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1 <?xml version="1.0"?> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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2 <!-- |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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3 # Copyright (C) 2015 INRA |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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4 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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5 # This program is free software: you can redistribute it and/or modify |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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6 # it under the terms of the GNU General Public License as published by |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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7 # the Free Software Foundation, either version 3 of the License, or |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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8 # (at your option) any later version. |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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9 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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10 # This program is distributed in the hope that it will be useful, |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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13 # GNU General Public License for more details. |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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14 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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15 # You should have received a copy of the GNU General Public License |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>. |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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17 --> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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18 <tool id="FROGS_filters" name="FROGS Filters" version="1.3.0"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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19 <description>Filters OTUs on several criteria.</description> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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20 <requirements> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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21 <requirement type="package" version="2.0.1">frogs</requirement> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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22 </requirements> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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23 <stdio> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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24 <exit_code range="1:" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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25 <exit_code range=":-1" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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26 </stdio> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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27 |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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28 <command> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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29 filters.py |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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30 --nb-cpus $nb_cpu |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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31 --input-biom $input_biom |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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32 --input-fasta $input_fasta |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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33 --output-fasta $output_fasta |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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34 --output-biom $output_biom |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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35 --excluded $output_excluded |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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36 --summary $output_summary |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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37 #if $contaminations_filter.contaminations_filter_isApplied == "yes" |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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38 --contaminant $contaminations_filter.contaminants_db |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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39 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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40 |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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41 #if $abundance_filters.abundance_filters_areApplied == "yes" |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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42 #if $abundance_filters.min_sample_presence |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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43 --min-sample-presence $abundance_filters.min_sample_presence |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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44 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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45 #if $abundance_filters.min_abundance |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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46 --min-abundance $abundance_filters.min_abundance |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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47 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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48 #if $abundance_filters.nb_biggest_otu |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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49 --nb-biggest-otu $abundance_filters.nb_biggest_otu |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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50 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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51 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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52 |
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53 #if $RDP_filters.RDP_filters_areApplied == "yes" |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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54 --min-rdp-bootstrap $RDP_filters.rdp_rank:$RDP_filters.rdp_bootstrap |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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55 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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56 |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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57 #if $blast_filters.blast_filters_areApplied == "yes" |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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58 #if $blast_filters.min_blast_length |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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59 --min-blast-length $blast_filters.min_blast_length |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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60 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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61 #if $blast_filters.max_blast_evalue |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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62 --max-blast-evalue $blast_filters.max_blast_evalue |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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63 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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64 #if $blast_filters.min_blast_identity |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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65 --min-blast-identity $blast_filters.min_blast_identity |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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66 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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67 #if $blast_filters.min_blast_coverage |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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68 --min-blast-coverage $blast_filters.min_blast_coverage |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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69 #end if |
76c750c5f0d1
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70 #end if |
76c750c5f0d1
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71 </command> |
76c750c5f0d1
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72 <inputs> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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73 <!-- Files --> |
76c750c5f0d1
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74 <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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75 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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76 |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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77 <!-- Parameters --> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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78 <param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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79 |
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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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80 <conditional name="abundance_filters"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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81 <param name="abundance_filters_areApplied" type="select" label=" *** THE FILTERS ON OTUS IN SAMPLES, OTUS SIZE and SEQUENCE PERCENTAGE" help="If you want to filter OTUs on their abundance and occurrence." > |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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82 <option value="no">No filters</option> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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83 <option value="yes">Apply filters</option> |
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84 </param> |
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85 <when value="no"></when> |
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86 <when value="yes"> |
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87 <param name="min_sample_presence" type="integer" optional="true" label="Minimum number of samples" size="5" help="Fill the field only if you want this treatment. Keep OTU present in at least this number of samples." /> |
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88 <param name="min_abundance" type="text" optional="true" label="Minimum proportion/number of sequences to keep OTU" size="5" help="Fill the field only if you want this treatment. Use decimal notation for proportion (example: 0.01 for keep OTU with at least 1% of all sequences) ; Use integer notation for number of sequence (example: 2 for keep OTU with at least 2 sequences, so remove single singleton)." /> |
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89 <param name="nb_biggest_otu" type="integer" optional="true" label="N biggest OTU" size="5" help="Fill the fields only if you want this treatment. Keep the N biggest OTU." /> |
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90 </when> |
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91 </conditional> |
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92 |
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93 <conditional name="RDP_filters"> |
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94 <param name="RDP_filters_areApplied" type="select" label=" *** THE FILTERS ON RDP" help="If you want to filter OTUs on their taxonomic affiliation produced by RDP."> |
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95 <option value="no">No filters</option> |
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96 <option value="yes">Apply filters</option> |
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97 </param> |
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98 <when value="no"></when> |
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99 <when value="yes"> |
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100 <param name="rdp_rank" type="select" label="Rank with the bootstrap filter" optional="true"> |
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101 <option value="Domain">Domain</option> |
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102 <option value="Phylum">Phylum</option> |
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103 <option value="Class">Class</option> |
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104 <option value="Order">Order</option> |
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105 <option value="Family">Family</option> |
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106 <option value="Genus">Genus</option> |
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107 <option value="Species">Species</option> |
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108 </param> |
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109 <param name="rdp_bootstrap" type="float" min="0.0" max="1.0" label="Minimum bootstrap % (between 0 and 1)" size="5" optional="true" /> |
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110 </when> |
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111 </conditional> |
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112 |
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113 <conditional name="blast_filters"> |
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114 <param name="blast_filters_areApplied" type="select" label=" *** THE FILTERS ON BLAST" help="If you want to filter OTUs on their taxonomic affiliation produced by Blast."> |
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115 <option value="no">No filters</option> |
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116 <option value="yes">Apply filters</option> |
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117 </param> |
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118 <when value="no"></when> |
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119 <when value="yes"> |
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120 <param name="max_blast_evalue" type="text" value="" label="Maximum e-value (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" /> |
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121 <param name="min_blast_identity" type="float" min="0.0" max="1.0" optional="true" label="Minimum identity % (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" /> |
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122 <param name="min_blast_coverage" type="float" min="0.0" max="1.0" optional="true" label="Minimum coverage % (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" /> |
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123 <param name="min_blast_length" type="integer" optional="true" label="Minimum alignment length" size="5" help="Fill the field only if you want this treatment" /> |
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124 </when> |
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125 </conditional> |
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126 |
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127 <conditional name="contaminations_filter"> |
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128 <param name="contaminations_filter_isApplied" type="select" label=" *** THE FILTERS ON CONTAMINATIONS" help="If you want to filter OTUs on classical contaminations."> |
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129 <option value="no">No filters</option> |
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130 <option value="yes">Apply filters</option> |
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131 </param> |
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132 <when value="no"></when> |
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133 <when value="yes"> |
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134 <param name="contaminants_db" type="select" label="Cotaminant databank" help="The phiX databank (the phiX is a control added in Illumina sequencing technologies)."> |
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135 <options from_file="phiX_db.loc"> |
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136 <column name="name" index="0"/> |
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137 <column name="value" index="1"/> |
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138 </options> |
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139 </param> |
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140 </when> |
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141 </conditional> |
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142 </inputs> |
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143 <outputs> |
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144 <data format="fasta" name="output_fasta" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta" /> |
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145 <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> |
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146 <data format="tabular" name="output_excluded" label="${tool.name}: excluded.tsv" from_work_dir="excluded.tsv" /> |
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147 <data format="html" name="output_summary" label="${tool.name}: report.html" from_work_dir="report.html" /> |
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148 </outputs> |
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149 <tests> |
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150 <test> |
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151 <param name="input_fasta" value="references/03-chimera.fasta" /> |
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152 <param name="input_biom" value="references/03-chimera.biom" /> |
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153 <conditional name="abundance_filters"> |
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154 <param name="abundance_filters_areApplied" value="yes" /> |
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155 <param name="min_abundance" value="0.00005" /> |
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156 <param name="min_sample_presence" value="3" /> |
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157 </conditional> |
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158 <output name="output_fasta" file="references/04-filters.fasta" /> |
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159 <output name="output_excluded" file="references/04-filters.excluded" /> |
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160 </test> |
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161 </tests> |
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162 <help> |
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163 |
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164 .. image:: static/images/FROGS_logo.png |
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165 :height: 144 |
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166 :width: 110 |
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167 |
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168 |
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169 |
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170 .. class:: infomark page-header h2 |
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171 |
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172 What it does |
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173 |
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174 Filter the OTUs of an abundance table according : |
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175 |
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176 -The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs. |
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177 |
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178 -The taxonomic affiliation produced by RDP: rank and bootstrap. |
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179 |
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180 -The taxonomic affiliation produced by Blast: e-value, percentage of identity, percentage of coverage and alignment length. |
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181 |
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182 -Contamination: phiX a control added in Illumina sequencing technologies. |
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183 |
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184 |
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185 |
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186 .. class:: infomark page-header h2 |
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187 |
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188 Inputs/outputs |
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189 |
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190 |
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191 .. class:: h3 |
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192 |
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193 Inputs |
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194 |
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195 **Sequence file**: |
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196 |
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197 The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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198 |
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199 **Abundance file**: |
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200 |
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201 The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). |
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202 |
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203 |
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204 .. class:: h3 |
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205 |
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206 Outputs |
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207 |
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208 **Sequence file** (sequences.fasta): |
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209 |
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210 The sequences after filtering (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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211 |
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212 **Abundance file** (abundance.biom): |
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213 |
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214 The abundance after filtering (format `BIOM <http://biom-format.org/>`_). |
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215 |
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216 **Excluded file** (excluded.txt): |
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217 |
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218 The list of the OTUs deleted by filters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). |
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219 |
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220 **Summary file** (report.html): |
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221 |
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222 The filters and the number of removed sequences (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). |
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223 |
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224 |
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225 |
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226 .. class:: infomark page-header h2 |
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227 |
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228 How it works |
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229 |
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230 |
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231 |
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232 |
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233 The OTUs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user. |
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234 |
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235 The BIOM abundance table and the fasta file are written again according to the OTUs kept. |
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236 |
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237 The OTUs discarded are listed in the excluded file. |
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238 |
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239 .. csv-table:: |
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240 :header: "Steps", "description" |
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241 :widths: 5, 150 |
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242 :class: table table-striped |
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243 |
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244 "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters an list of the OTUs to remove is generated." |
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245 "2", "All the OTUs tagged to remove by at least one filter are removed." |
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246 "3", "If the filter to select the N most abundant OTUs is filled it is applied." |
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247 |
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248 |
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249 |
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250 .. class:: infomark page-header h2 |
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251 |
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252 Advices |
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253 |
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254 Please check that the input fasta file and the input BIOM file correspond to the same OTUs. |
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255 |
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256 Examples for the filters on abundance and occurence of the OTUs : |
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257 |
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258 -To keep the filters that are present in 5 samples, fill the corresponding field with "5". |
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259 |
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260 -To display the 20 biggest OTU, fill the corresponding field with "20". |
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261 |
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262 -To filter on abundance, we advise you to specify 0.005%. It seems to be the optimal threshold (`Bokulich *et al*, 2013 <http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html>`_ ). |
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263 |
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264 If you use "FROGS Filters" before "FROGS Affiliation", the filters on RDP and Blast are useless. |
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265 |
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266 ---- |
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267 |
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268 **Contact** |
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269 |
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270 Contacts: frogs@inra.fr |
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271 |
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272 Repository: https://github.com/geraldinepascal/FROGS |
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273 |
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274 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf |
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275 |
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276 Depending on the help provided you can cite us in acknowledgements, references or both. |
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277 </help> |
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278 <citations> |
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279 <citation type="doi">10.1093/bioinformatics/btx791</citation> |
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280 <citation type="doi">10.1128/AEM.01043-13</citation> |
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281 <citation type="doi">10.14806/ej.17.1.200</citation> |
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282 <citation type="doi">10.1093/bioinformatics/btr507</citation> |
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283 </citations> |
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284 |
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285 </tool> |