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planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
author ecology
date Tue, 25 Apr 2023 10:05:14 +0000
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3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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1 <tool id="aligned_to_consensus" name="Consensus sequence from aligned FASTA" version="@VERSION@">
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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2 <description></description>
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3 <macros>
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4 <import>consalign_macros.xml</import>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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5 </macros>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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6 <requirements>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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7 <requirement type="package" version="0.1.4">r-bioseq</requirement>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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8 <requirement type="package" version="1.0.14">r-ptxqc</requirement>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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9 </requirements>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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10 <command detect_errors="exit_code"><![CDATA[
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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11 Rscript
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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12 '$__tool_directory__/consensus_from_alignments.R'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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13 '$input'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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14 '$seqtype'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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15 '$method'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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16 '$gaps'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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17 '$outog'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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18 '$output'
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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19 ]]>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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20 </command>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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21 <inputs>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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22 <param name="input" type="data" format="fasta" label="Input fasta file with at least two sequences"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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23 <param name="seqtype" type="select" label="Type of sequence" multiple="false" optional="false" display="radio">
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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24 <option value="DNA" selected="true">DNA</option>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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25 <option value="RNA">RNA</option>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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26 <option value="AA">Amino Acid</option>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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27 </param>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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28 <param name="method" type="select" label="Consensus method when differences are found between sequences" multiple="false" optional="false" display="radio">
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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29 <option value="chr_ambiguity" selected="true">Use an ambiguous nucleotide</option>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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30 <option value="chr_majority">Use the most frequent nucleotide</option>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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31 </param>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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32 <param name="gaps" type="boolean" checked="no" label="Take account of gaps?" help="/!\ If gaps are at the same place in all the sequences don't check 'no', you'll face an error"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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33 <param name="outog" type="boolean" checked="no" label="Output consensus sequence AND original sequences in the FASTA file?" help="/!\ If gaps are at the same place in all the sequences don't check 'no', you'll face an error"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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34 </inputs>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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35 <outputs>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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36 <data name="output" from_work_dir="output.fasta" format="fasta" label="Consensus sequence of ${input.display_name}"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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37 </outputs>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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38 <tests>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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39 <test>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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40 <param name="input" value="test_file.fasta"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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41 <param name="seqtype" value="DNA"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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42 <param name="method" value="chr_ambiguity"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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43 <param name="gaps" value="false"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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44 <param name="outog" value="false"/>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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45 <output name="output">
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46 <assert_contents>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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47 <has_n_lines n="2"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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53 =====================================================
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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54 Get consensus sequence from several aligned sequences
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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55 =====================================================
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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56
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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57 This tool uses the seq_consensus function from the bioseq package. @WARNING@ If gaps are at the same place in all the sequences don't check 'no' in the gaps parameter,
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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58 you'll face an error.
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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59
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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60 Input can be any fasta file containing at least two aligned sequences.
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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61
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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62 Output is a FASTA file containing the computed consensus sequence (along with original sequences if you want to).
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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63 ]]></help>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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64 <citations>
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65 <citation type="doi">10.1111/2041-210X.13490</citation>
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66 </citations>
3196a3144eb7 planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments commit ecc21de8f368c6a95c57d4e6511ed42af9e72a66
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67 </tool>