Mercurial > repos > frogs > frogs_2_0_0
annotate remove_chimera.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
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9 # |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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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
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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
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18 <tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="1.3.0"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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19 <description>Step 3 in metagenomics analysis : Remove PCR chimera in each sample.</description> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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20 <requirements> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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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
frogs
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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 <command> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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28 remove_chimera.py |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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29 --nb-cpus $nb_cpus |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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30 --input-fasta $sequence_file --non-chimera $non_chimera_fasta |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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31 --summary $summary_file |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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32 #if $abundance_type.abundance_type_selected == "biom" |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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33 --input-biom $abundance_biom |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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34 --out-abundance $out_abundance_biom |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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35 #else |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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36 --input-count $abundance_count |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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37 --out-abundance $out_abundance_count |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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38 #end if |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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39 </command> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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40 <inputs> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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41 <!-- Files --> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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42 <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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43 <conditional name="abundance_type"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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44 <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored."> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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45 <option value="biom" selected="true">BIOM file</option> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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46 <option value="count">TSV file</option> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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47 </param> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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48 <when value="biom"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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49 <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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50 </when> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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51 <when value="count"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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52 <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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53 </when> |
76c750c5f0d1
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54 </conditional> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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55 <!-- Parameters --> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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56 <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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57 <!-- |
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58 <param name="size_separator" type="text" label="Size separator" help="Fill this input only if the IDs of sequences in fasta store the abundance as suffix. Example: 'Cluster_1;size=10' => ';size='" value="" optional="true" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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59 --> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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60 </inputs> |
76c750c5f0d1
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61 <outputs> |
76c750c5f0d1
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62 <data format="fasta" name="non_chimera_fasta" label="${tool.name}: non_chimera.fasta" from_work_dir="non_chimera.fasta"/> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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63 <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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64 <filter>abundance_type['abundance_type_selected'] == "biom"</filter> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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65 </data> |
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66 <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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67 <filter>abundance_type['abundance_type_selected'] == "count"</filter> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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68 </data> |
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69 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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70 </outputs> |
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71 <tests> |
76c750c5f0d1
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72 <test> |
76c750c5f0d1
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73 <param name="sequence_file" value="references/02-clustering.fasta"/> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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74 <conditional name="abundance_type"> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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75 <param name="abundance_type_selected" value="biom"/> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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76 <param name="abundance_biom" value="references/02-clustering.biom" /> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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77 </conditional> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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78 <output name="non_chimera_fasta" file="references/03-chimera.fasta"/> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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79 </test> |
76c750c5f0d1
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80 </tests> |
76c750c5f0d1
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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81 <help> |
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82 |
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83 .. image:: static/images/FROGS_logo.png |
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84 :height: 144 |
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85 :width: 110 |
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86 |
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87 |
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88 .. class:: infomark page-header h2 |
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89 |
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90 What it does |
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91 |
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92 Remove chimeric sequences by sample. |
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93 |
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94 |
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95 .. class:: infomark page-header h2 |
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96 |
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97 Context |
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98 |
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99 Chimeras are sequences formed from two or more biological sequences joined together. |
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100 |
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101 The majority of these anomalous sequences are formed from an incomplete extension during a PCR cycle. During subsequent cycles, a partially extended strand can bind to a template derived from a different but similar sequence. |
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102 |
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103 This phenomena is particularly common in amplicon sequencing where closely related sequences are amplified. |
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104 |
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105 |
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106 .. class:: infomark page-header h2 |
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107 |
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108 Inputs/Outputs |
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109 |
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110 .. class:: h3 |
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111 |
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112 Inputs |
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113 |
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114 **Sequence file**: |
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115 |
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116 The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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117 |
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118 **Abundance file**: |
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119 |
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120 The abundance of each cluster in each sample (format `BIOM <http://biom-format.org/>`_). |
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121 |
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122 OR |
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123 |
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124 The abundance of each sequence in each sample (format `TSV <https://en.wikipedia.org/wiki/Tab-separated_values>`_). This type of file is produced by *FROGS pre-process*. |
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125 |
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126 Example:: |
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127 |
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128 #id splA splB |
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129 seq1 1289 2901 |
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130 seq2 3415 0 |
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131 |
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132 .. class:: h3 |
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133 |
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134 Outputs |
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135 |
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136 **Sequence file** (non_chimera.fasta): |
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137 |
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138 The sequence file with only non-chimera (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). |
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139 |
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140 **Abundance file** (non_chimera.biom or non_chimera.tsv): |
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141 |
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142 The abundance file with only non-chimera (format the same of the abundance input). |
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143 |
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144 **Summary file** (report.html): |
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145 |
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146 This file presents the number of removed elements (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). |
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147 |
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148 |
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149 .. class:: infomark page-header h2 |
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150 |
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151 How it works |
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152 |
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153 .. csv-table:: |
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154 :header: "Steps", "Description" |
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155 :widths: 10, 90 |
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156 :class: table table-striped |
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157 |
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158 "1", "Split input data by sample (classicaly the PCR is realised by sample)." |
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159 "2", "Find chimera in each sample (`vsearch <https://github.com/torognes/vsearch>`_)." |
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160 "3", "Remove the sequences identify as chimera in all samples where they are present." |
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161 |
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162 |
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163 ---- |
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164 |
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165 **Contact** |
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166 |
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167 Contacts: frogs@inra.fr |
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168 |
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169 Repository: https://github.com/geraldinepascal/FROGS |
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170 |
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171 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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172 |
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173 Depending on the help provided you can cite us in acknowledgements, references or both. |
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174 </help> |
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175 <citations> |
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176 <citation type="doi">10.7287/peerj.preprints.386v1</citation> |
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177 </citations> |
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178 </tool> |