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annotate viralverify.xml @ 0:ddbdb0763437 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
author iuc
date Sun, 06 Jul 2025 18:23:42 +0000
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0
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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1 <tool id="viralverify" name="viralverify" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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2 <description>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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3 Classify contigs as viral, non-viral or uncertain, based on gene content
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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4 </description>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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5 <macros>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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6 <token name="@TOOL_VERSION@">1.1</token>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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7 <token name="@VERSION_SUFFIX@">0</token>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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8 <token name="@PROFILE@">23.2</token>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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9 </macros>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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10 <requirements>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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11 <requirement type="package" version="@TOOL_VERSION@">viralverify</requirement>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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12 </requirements>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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13 <command detect_errors="exit_code"><![CDATA[
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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14 ln -s '$input_fasta' 'contigs.fasta' &&
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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15 viralverify
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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16 -f 'contigs.fasta'
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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17 -o .
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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18 --hmm '$hmm'
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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19 ## OPTIONNAL BLAST NOT TESTED YET
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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20 ## #if '$locdb'
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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21 ## --db $locdb
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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22 ## #end if
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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23 ## #if '$histdb'
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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24 ## --db '$histdb'
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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25 ## #end if
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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26 --thr $thr
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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27 -t \${GALAXY_SLOTS:-1}
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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28 $plasmid_detect
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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29 ]]></command>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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30 <inputs>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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31 <!--MANDATORY :-->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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32 <!-- INPUT FASTA FILE-->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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33 <param name="input_fasta" type="data" format="fasta" label="Fasta file containing contigs to predict"/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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34 <!-- INPUT HMM PROFILE -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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35 <param argument="--hmm" type="data" format="hmm3" label="HMM profile"/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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36 <!-- OPTIONAL : -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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37 <!-- RUN BLAST -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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38 <!-- Trying to implement the - -db option here but im currently unable to test it with a blastdbn file -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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39 <!-- <conditional name="do_run_blast">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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40 <param name="runblast" type="select" label="Run BLAST on input contigs?" >
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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41 <option value="locdb" selected="true">With locally installed BLAST database </option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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42 <option value="histdb" selected="false">With BLAST database from your history </option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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43 <option value="no_blast">No </option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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44 </param>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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45 <when value="locdb">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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46 <param name="database" type="select" multiple="true" optional="false" label="Nucleotide BLAST database">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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47 <options from_data_table="blastdb" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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48 </param>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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49 <param name="histdb" type="hidden" value="" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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50 <param name="subject" type="hidden" value="" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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51 </when>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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52 <when value="histdb">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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53 <param name="database" type="hidden" value="" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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54 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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55 <param name="subject" type="hidden" value="" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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56 </when>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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57 <when value="no_blast"/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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58 </conditional> -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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59 <!-- RUN PLASMID DETECTION -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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60 <param name="plasmid_detect" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable plasmid prediction?"/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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61 <!-- SENSITIVITY THRESHOLD -->
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62 <param argument="--thr" type="integer" value="7" label="Sensitivity threshold" help="Minimal absolute score to classify sequence."/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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63 <!--OUTPUTS CONTROL-->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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64 <param name="outputs" type="select" multiple="true" label="Output files to generate" help="If plasmid prediction is not enabled, plasmid outputs won't be generated.">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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65 <option value="viral_pred" selected="true" >Predicted viral contigs (FASTA)</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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66 <option value="Unc_viral_pred" selected="true">Uncertain viral contigs (FASTA)</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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67 <option value="plasmid_pred" selected="false">Predicted plasmid contigs(FASTA) - plasmid prediction must be checked</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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68 <option value="Unc_plasmid_pred" selected="false">Uncertain plasmid contigs (FASTA)</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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69 <option value="chromosomal_pred" selected="true">Predicted chromosomal contigs(FASTA) - plasmid prediction must be checked</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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70 <option value="result_table" selected="true">Table with contig predictions</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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71 <option value="prodigal_report" selected="false">Prodigal report</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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72 <option value="prodigal_genbank" selected="false">Prodigal GenBank file</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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73 <option value="prodigal_proteins_circ" selected="false">Prodigal proteins (circular)</option>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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74 <option value="prodigal_proteins" selected="false">Prodigal proteins (linear)</option>
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75 <option value="hmmsearch_report" selected="false">HMM search report</option>
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76 <option value="hmmsearch_domtblout" selected="false">hmmsearch output</option>
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77 </param>
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78 </inputs>
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79 <outputs>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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80 <!-- VIRAL PREDICTIONS -->
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81 <data name="predicted_viral" format="fasta" label="${tool.name} on ${on_string}: Predicted viral contigs" from_work_dir="Prediction_results_fasta/contigs_virus.fasta">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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82 <filter>outputs and 'viral_pred' in outputs</filter>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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83 </data>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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84 <data name="uncertain_viral" format="fasta" label="${tool.name} on ${on_string}: Uncertain viral contigs" from_work_dir="Prediction_results_fasta/contigs_virus_uncertain.fasta">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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85 <filter>outputs and 'Unc_viral_pred' in outputs</filter>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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86 </data>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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87 <!-- PLASMID PREDICTIONS -->
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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88 <data name="predicted_plasmid" format="fasta" label="${tool.name} on ${on_string}: Predicted plasmid contigs" from_work_dir="Prediction_results_fasta/contigs_plasmid.fasta">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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89 <filter>outputs and 'plasmid_pred' in outputs</filter>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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90 <filter>plasmid_detect</filter>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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91 </data>
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92 <data name="uncertain_plasmid" format="fasta" label="${tool.name} on ${on_string}: Uncertain plasmid contigs" from_work_dir="Prediction_results_fasta/contigs_plasmid_uncertain.fasta">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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93 <filter>outputs and 'Unc_plasmid_pred' in outputs</filter>
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94 <filter>plasmid_detect</filter>
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95 </data>
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96 <!-- CHROMOSOME PREDICTIONS -->
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97 <data name="chromosomal" format="fasta" label="${tool.name} on ${on_string}: Predicted chromosomal contig contigs" from_work_dir="Prediction_results_fasta/contigs_uncertain_plasmid.fasta">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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98 <filter>outputs and 'chromosomal_pred' in outputs</filter>
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99 </data>
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100 <!-- TABLE ALL PREDICTIONS + FEATURES -->
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101 <data name="result_table" format="csv" label="${tool.name} on ${on_string}: Table with contig predictions" from_work_dir="contigs_result_table.csv">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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102 <filter>outputs and 'result_table' in outputs</filter>
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103 </data>
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104 <!-- PRODIGAL OUTPUTS -->
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105 <data name="prodigal_report" format="txt" label="${tool.name} on ${on_string}: Prodigal report" from_work_dir="contigs_prodigal.log">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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106 <filter>outputs and 'prodigal_report' in outputs</filter>
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107 </data>
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108 <data name="prodigal_genbank" format="genbank" label="${tool.name} on ${on_string}: Prodigal genbank file" from_work_dir="contigs_genes.fa">
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109 <filter>outputs and 'prodigal_genbank' in outputs</filter>
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110 </data>
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111 <data name="prodigal_proteins_circ" format="fasta" label="${tool.name} on ${on_string}: Prodigal proteins (circular)" from_work_dir="contigs_proteins_circ.fa">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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112 <filter>outputs and 'prodigal_proteins_circ' in outputs</filter>
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113 </data>
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114 <data name="prodigal_proteins" format="fasta" label="${tool.name} on ${on_string}: Prodigal proteins (linear)" from_work_dir="contigs_proteins.fa">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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115 <filter>outputs and 'prodigal_proteins' in outputs</filter>
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116 </data>
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117 <!-- HMMSEARCH OUTPUTS -->
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118 <data name="hmmsearch_report" format="txt" label="${tool.name} on ${on_string}: HMM search report" from_work_dir="contigs_out_pfam.txt">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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119 <filter>outputs and 'hmmsearch_report' in outputs</filter>
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120 </data>
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121 <data name="hmmsearch_domtblout" format="txt" label="${tool.name} on ${on_string}: hmmsearch output" from_work_dir="contigs_domtblout">
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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122 <filter>outputs and 'hmmsearch_domtblout' in outputs</filter>
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123 </data>
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124 </outputs>
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125 <tests>
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126 <test expect_num_outputs="12">
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127 <param name="input_fasta" value="test.fa"/>
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128 <param name="hmm" value="test.hmm"/>
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129 <param name="plasmid_detect" value="true"/>
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130 <param name="thr" value="7"/>
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131 <param name="outputs" value="viral_pred,Unc_viral_pred,chromosomal_pred,plasmid_pred,Unc_plasmid_pred,result_table,prodigal_report,prodigal_genbank,prodigal_proteins_circ,prodigal_proteins,hmmsearch_report,hmmsearch_domtblout"/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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132 <!-- <conditional name="do_run_blast">
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133 <param name="runblast" value="no_blast" />
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134 </conditional> -->
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135 <output name="uncertain_viral">
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136 <assert_contents>
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137 <has_text text=">NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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138 <has_text text=">NC_001416.1 Enterobacteria phage lambda, complete genome" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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139 <has_text text=">NZ_CP021331.1 Maritalea myrionectae strain HL2708#5 plasmid pHL2708X3, complete sequence" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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140 <has_text text=">CP045262.1 Yersinia pestis strain SCPM-O-B-5942 (I-2638) plasmid pPCP, complete sequence" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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141 <has_text text=">NC_000913.3:1-30000 Escherichia coli str. K-12 substr. MG1655, complete genome" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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142 </assert_contents>
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143 </output>
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144 <output name="predicted_viral">
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145 <assert_contents>
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146 <not_has_text text=">NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome" />
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147 </assert_contents>
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148 </output>
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149 <output name="predicted_plasmid">
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150 <assert_contents>
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151 <not_has_text text=">NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome" />
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152 </assert_contents>
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153 </output>
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154 <output name="uncertain_plasmid">
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155 <assert_contents>
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156 <not_has_text text=">NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome" />
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157 </assert_contents>
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158 </output>
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159 <output name="chromosomal">
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160 <assert_contents>
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161 <not_has_text text=">NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome" />
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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162 </assert_contents>
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163 </output>
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164 <output name="result_table">
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165 <assert_contents>
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166 <has_text text="Contig name,Prediction,Length,Circular,Score,Pfam hits"/>
ddbdb0763437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify commit daf56661e044ace256c1fd635b494d8998af3201
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167 </assert_contents>
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168 </output>
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169 <output name="hmmsearch_domtblout">
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170 <assert_contents>
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171 <has_text text="# Program:"/>
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172 </assert_contents>
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173 </output>
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174 <!-- Somehow the output below is empty while all others are correponding to the expected output-->
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175 <!-- <output name="hmmsearch_report">
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176 <assert_contents>
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177 <has_text text="# hmmsearch :: search profile(s) against a sequence database"/>
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178 </assert_contents>
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179 </output> -->
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180 <output name="prodigal_genbank">
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181 <assert_contents>
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182 <has_text text="NC_045512.2 Severe acute respiratory syndrome"/>
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183 </assert_contents>
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184 </output>
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185 <output name="prodigal_report">
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186 <assert_contents>
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187 <has_text text="PRODIGAL v2.6.3 [February, 2016]"/>
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188 </assert_contents>
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189 </output>
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190 <output name="prodigal_proteins_circ">
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191 <assert_contents>
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192 <has_text text=">NC_045512.2_1"/>
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193 </assert_contents>
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194 </output>
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195 <output name="prodigal_proteins">
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196 <assert_contents>
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197 <has_text text=">NC_045512.2_1"/>
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198 </assert_contents>
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199 </output>
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200 </test>
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201 </tests>
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202 <help>
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203 <![CDATA[
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204 viralVerify classifies contigs (output of metaviralSPAdes or other assemblers) as viral, non-viral or uncertain, based on gene content. Also for non-viral contigs it can optionally provide plasmid/non-plasmid classification.
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205
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206 viralVerify predicts genes in the contig using Prodigal in the metagenomic mode, runs hmmsearch on the predicted proteins and classifies the contig as viral or non-viral by applying the Naive Bayes classifier (NBC). For the set of predicted HMMs, viralVerify uses trained NBC to classify this set to be viral or chromosomal.
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207
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208 To improve results in the case of metagenomes with possible host contamination, we recommend users to filter out reads that align to the host genome prior to assembly. Since viralVerify is based on gene classification, it can be used on contigs on any length, and short viruses can be detected as long as they contain a recognizable virus-specific gene.
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209
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210 More informations about this tool on the `viralVerify package <https://github.com/ablab/viralVerify>`_ and the `viralVerify bioconda package <https://anaconda.org/bioconda/viralverify>`_.
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211 ]]>
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212 </help>
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213 <citations>
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214 <citation type="bibtex">
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215 @misc{viralverify2023,
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216 author = {Mikhail Raiko,Dmitry Antipov,Sam Nooij},
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217 title = {ViralVerify: Classify contigs as viral or non-viral based on gene content},
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218 year = {2021},
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219 howpublished = {\url{https://github.com/ablab/viralVerify/}}
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220 }
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221 </citation>
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222 </citations>
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223 </tool>