Mercurial > repos > frogs > frogs_3_1_0
annotate filters.xml @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author | frogs |
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date | Thu, 28 Feb 2019 10:14:49 -0500 |
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0
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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1 <?xml version="1.0"?> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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2 <!-- |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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3 # Copyright (C) 2015 INRA |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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4 # |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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5 # This program is free software: you can redistribute it and/or modify |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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6 # it under the terms of the GNU General Public License as published by |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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7 # the Free Software Foundation, either version 3 of the License, or |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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8 # (at your option) any later version. |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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9 # |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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10 # This program is distributed in the hope that it will be useful, |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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13 # GNU General Public License for more details. |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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14 # |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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15 # You should have received a copy of the GNU General Public License |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>. |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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17 --> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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18 <tool id="FROGS_filters" name="FROGS Filters" version="3.1"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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19 <description>Filters OTUs on several criteria.</description> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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20 <requirements> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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21 <requirement type="package" version="3.1.0">frogs</requirement> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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22 </requirements> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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23 <stdio> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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24 <exit_code range="1:" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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25 <exit_code range=":-1" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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26 </stdio> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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27 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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28 <command> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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29 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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30 filters.py |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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31 --nb-cpus \${GALAXY_SLOTS:-1} |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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32 --input-biom $input_biom |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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33 --input-fasta $input_fasta |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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34 --output-fasta $output_fasta |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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35 --output-biom $output_biom |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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36 --excluded $output_excluded |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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37 --summary $output_summary |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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38 #if $contaminations_filter.contaminations_filter_isApplied == "yes" |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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39 #set $contaminants_filename = str( $contaminations_filter.contaminants_db.fields.path ) |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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40 --contaminant $contaminants_filename |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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41 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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42 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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43 #if $abundance_filters.abundance_filters_areApplied == "yes" |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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44 #if $abundance_filters.min_sample_presence |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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45 --min-sample-presence $abundance_filters.min_sample_presence |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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46 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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47 #if $abundance_filters.min_abundance |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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48 --min-abundance $abundance_filters.min_abundance |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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49 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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50 #if $abundance_filters.nb_biggest_otu |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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51 --nb-biggest-otu $abundance_filters.nb_biggest_otu |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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52 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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53 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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54 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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55 #if $RDP_filters.RDP_filters_areApplied == "yes" |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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56 --min-rdp-bootstrap $RDP_filters.rdp_rank:$RDP_filters.rdp_bootstrap |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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57 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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58 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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59 #if $blast_filters.blast_filters_areApplied == "yes" |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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60 #if $blast_filters.min_blast_length |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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61 --min-blast-length $blast_filters.min_blast_length |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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62 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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63 #if $blast_filters.max_blast_evalue |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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64 --max-blast-evalue $blast_filters.max_blast_evalue |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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65 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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66 #if $blast_filters.min_blast_identity |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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67 --min-blast-identity $blast_filters.min_blast_identity |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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68 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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69 #if $blast_filters.min_blast_coverage |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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70 --min-blast-coverage $blast_filters.min_blast_coverage |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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71 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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72 #end if |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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73 </command> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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74 <inputs> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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75 <!-- Files --> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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76 <param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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77 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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78 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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79 <conditional name="abundance_filters"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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80 <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." > |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
81 <option value="no">No filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
82 <option value="yes">Apply filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
83 </param> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
84 <when value="no"></when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
85 <when value="yes"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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86 <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." /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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87 <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)." /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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88 <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." /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
89 </when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
90 </conditional> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
91 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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92 <conditional name="RDP_filters"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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93 <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."> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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94 <option value="no">No filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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95 <option value="yes">Apply filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
96 </param> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
97 <when value="no"></when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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98 <when value="yes"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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99 <param name="rdp_rank" type="select" label="Rank with the bootstrap filter" optional="true"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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100 <option value="Domain">Domain</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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changeset
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101 <option value="Phylum">Phylum</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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102 <option value="Class">Class</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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diff
changeset
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103 <option value="Order">Order</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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104 <option value="Family">Family</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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changeset
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105 <option value="Genus">Genus</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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changeset
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106 <option value="Species">Species</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
107 </param> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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108 <param name="rdp_bootstrap" type="float" min="0.0" max="1.0" label="Minimum bootstrap % (between 0 and 1)" size="5" optional="true" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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109 </when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
110 </conditional> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
111 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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112 <conditional name="blast_filters"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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113 <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."> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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diff
changeset
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114 <option value="no">No filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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115 <option value="yes">Apply filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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changeset
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116 </param> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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117 <when value="no"></when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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118 <when value="yes"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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119 <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" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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120 <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" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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121 <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" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
122 <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" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
123 </when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
124 </conditional> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
125 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
126 <conditional name="contaminations_filter"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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127 <param name="contaminations_filter_isApplied" type="select" label="Contaminant databank" help="The phiX databank (the phiX is a control added in Illumina sequencing technologies)."> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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diff
changeset
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128 <option value="no">No filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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129 <option value="yes">Apply filters</option> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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130 </param> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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131 <when value="no"></when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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132 <when value="yes"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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133 <param name="contaminants_db" type="select" label="Contaminant databank" help="The phiX databank (the phiX is a control added in Illumina sequencing technologies)."> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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134 <options from_data_table="phiX_db"></options> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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135 <validator type="no_options" message="A built-in database is not available" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
136 </param> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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137 </when> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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138 </conditional> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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139 </inputs> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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140 <outputs> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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141 <data format="fasta" name="output_fasta" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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142 <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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143 <data format="tabular" name="output_excluded" label="${tool.name}: excluded.tsv" from_work_dir="excluded.tsv" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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144 <data format="html" name="output_summary" label="${tool.name}: report.html" from_work_dir="report.html" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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145 </outputs> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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146 <tests> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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changeset
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147 <test> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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148 <param name="input_fasta" value="references/03-chimera.fasta" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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149 <param name="input_biom" value="references/03-chimera.biom" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
|
150 <conditional name="abundance_filters"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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151 <param name="abundance_filters_areApplied" value="yes" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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152 <param name="min_abundance" value="0.00005" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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153 <param name="min_sample_presence" value="3" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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154 </conditional> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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155 <conditional name="contaminations_filter"> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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changeset
|
156 <param name="contaminations_filter_isApplied" value="yes" /> |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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157 <param name="contaminants_db" value="phiX_test" /> |
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158 </conditional> |
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159 <output name="output_fasta" file="references/04-filters.fasta" /> |
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160 <output name="output_excluded" file="references/04-filters.excluded" /> |
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161 </test> |
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162 </tests> |
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163 <help> |
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164 |
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165 .. image:: static/images/frogs_images/FROGS_logo.png |
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166 :height: 144 |
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167 :width: 110 |
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168 |
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169 |
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170 |
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171 .. class:: infomark page-header h2 |
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172 |
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173 What it does |
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174 |
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175 Filter the OTUs of an abundance table according : |
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176 |
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177 -The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs. |
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178 |
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179 -The taxonomic affiliation produced by RDP: rank and bootstrap. |
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180 |
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181 -The taxonomic affiliation produced by Blast: e-value, percentage of identity, percentage of coverage and alignment length. |
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182 |
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183 -Contamination: phiX a control added in Illumina sequencing technologies. |
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184 |
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185 |
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186 |
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187 .. class:: infomark page-header h2 |
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188 |
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189 Inputs/outputs |
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190 |
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191 |
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192 .. class:: h3 |
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193 |
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194 Inputs |
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195 |
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196 **Sequence file**: |
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197 |
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198 The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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199 |
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200 **Abundance file**: |
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201 |
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202 The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). |
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203 |
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204 |
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205 .. class:: h3 |
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206 |
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207 Outputs |
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208 |
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209 **Sequence file** (sequences.fasta): |
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210 |
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211 The sequences after filtering (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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212 |
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213 **Abundance file** (abundance.biom): |
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214 |
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215 The abundance after filtering (format `BIOM <http://biom-format.org/>`_). |
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216 |
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217 **Excluded file** (excluded.txt): |
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218 |
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219 The list of the OTUs deleted by filters (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). |
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220 |
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221 **Summary file** (report.html): |
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222 |
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223 The filters and the number of removed sequences (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). |
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224 |
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225 |
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226 |
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227 .. class:: infomark page-header h2 |
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228 |
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229 How it works |
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230 |
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231 |
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232 |
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233 |
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234 The OTUs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user. |
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235 |
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236 The BIOM abundance table and the fasta file are written again according to the OTUs kept. |
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237 |
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238 The OTUs discarded are listed in the excluded file. |
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239 |
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240 .. csv-table:: |
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241 :header: "Steps", "description" |
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242 :widths: 5, 150 |
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243 :class: table table-striped |
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244 |
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245 "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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246 "2", "All the OTUs tagged to remove by at least one filter are removed." |
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247 "3", "If the filter to select the N most abundant OTUs is filled it is applied." |
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248 |
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249 |
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250 |
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251 .. class:: infomark page-header h2 |
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252 |
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253 Advices |
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254 |
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255 Please check that the input fasta file and the input BIOM file correspond to the same OTUs. |
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256 |
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257 Examples for the filters on abundance and occurence of the OTUs : |
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258 |
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259 -To keep the filters that are present in 5 samples, fill the corresponding field with "5". |
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260 |
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261 -To display the 20 biggest OTU, fill the corresponding field with "20". |
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262 |
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263 -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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264 |
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265 If you use "FROGS Filters" before "FROGS Affiliation", the filters on RDP and Blast are useless. |
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266 |
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267 ---- |
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268 |
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269 **Contact** |
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270 |
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271 Contacts: frogs@inra.fr |
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272 |
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273 Repository: https://github.com/geraldinepascal/FROGS |
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274 website: http://frogs.toulouse.inra.fr/ |
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275 |
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276 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* |
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277 |
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278 </help> |
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279 <citations> |
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280 <citation type="doi">10.1093/bioinformatics/btx791</citation> |
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281 </citations> |
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282 </tool> |