Mercurial > repos > iuc > virannot_blast2tsv

annotate virAnnot_blast2tsv.xml @ 1:88ebde55bef8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 48a3a1fa033745898a131f9dca7132947683c02f
author iuc
date Sat, 18 May 2024 18:14:54 +0000
parents e889010415a1
children 77c3ef9b0ed7
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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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1 <tool id="virannot_blast2tsv" name="virAnnot Blast2tsv" version="1.0.0+galaxy0" profile="21.05">
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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2 <description>convert XML blast results to tabular file with taxonomic informations</description>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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3 <macros>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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4 <import>macros.xml</import>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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5 </macros>
1
88ebde55bef8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 48a3a1fa033745898a131f9dca7132947683c02f
iuc
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6 <expand macro="xrefs"/>
0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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7 <expand macro="requirements" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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8 <required_files>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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9 <include path="blast2tsv.py" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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10 </required_files>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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11 <command detect_errors="aggressive"><![CDATA[
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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12 python '$__tool_directory__/blast2tsv.py'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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13 -x '$blast_xml'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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14 -c '$contigs'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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15 -a '$blast_type'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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16 -me '$max_evalue'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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17 #if $read_nb
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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18 -rn '$read_nb'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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19 #end if
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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20 ]]></command>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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21 <inputs>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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22 <param type="data" name="blast_xml" format="blastxml" label="Blast results file" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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23 <param type="data" name="contigs" format="fasta" label="Contigs" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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24 <param type="select" name="blast_type" label="Type of blast">
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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25 <option value="BLASTX">BLASTX</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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26 <option value="BLASTP">BLASTP</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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27 <option value="TBLASTX" selected="true">TBLASTX</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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28 <option value="BLASTN">BLASTN</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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29 <option value="DIAMOND">DIAMOND</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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30 </param>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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31 <param type="select" name="max_evalue" label="Maximum evalue">
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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32 <option value="0">0</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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33 <option value="0.1">0.1</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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34 <option value="0.01">0.01</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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35 <option value="0.001" selected="true">0.001</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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36 <option value="0.0001">0.0001</option>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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37 </param>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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38 <param type="data" name="read_nb" format="tabular" label="Read number file" optional="true" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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39 </inputs>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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40 <outputs>
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41 <data name="out_annotation" format="tabular" from_work_dir="blast2tsv/blast2tsv_output.tab" label="${tool.name} on ${on_string} : annotation" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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42 <data name="out_reads" format="tabular" from_work_dir="blast2tsv/blast2tsv_reads.txt" label="${tool.name} on ${on_string} : output reads" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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43 <data name="out_contigs" format="tabular" from_work_dir="blast2tsv/blast2tsv_contigs.txt" label="${tool.name} on ${on_string} : output contigs" />
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="blast_xml" value="blast2tsv_input.xml"/>
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48 <param name="contigs" value="blast2tsv_contigs.fa"/>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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49 <param name="blast_type" value="TBLASTX"/>
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50 <param name="max_evalue" value="0.001"/>
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51 <output name="out_annotation" file="blast2tsv_output.tab">
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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52 <assert_contents>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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53 <has_n_columns n="16" />
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54 <has_n_lines n="6" />
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="blast_xml" value="blast2tsv_input.xml"/>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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60 <param name="contigs" value="blast2tsv_contigs.fa"/>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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61 <param name="blast_type" value="TBLASTX"/>
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62 <param name="max_evalue" value="0.001"/>
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63 <output name="out_annotation" file="blast2tsv_output.tab">
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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64 <assert_contents>
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65 <has_text text="NC_011554" />
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66 </assert_contents>
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67 </output>
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68 </test>
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69 <test>
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70 <param name="blast_xml" value="blast2tsv_input.xml"/>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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71 <param name="contigs" value="blast2tsv_contigs.fa"/>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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72 <param name="blast_type" value="TBLASTX"/>
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73 <param name="max_evalue" value="0.001"/>
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74 <param name="read_nb" value="blast2tsv_read_nb.tab"/>
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75 <output name="out_annotation" file="blast2tsv_output_with_rn.tab">
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76 <assert_contents>
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77 <has_text text="402" />
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78 </assert_contents>
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79 </output>
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80 <output name="out_annotation" file="blast2tsv_reads_with_rn.txt">
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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81 <assert_contents>
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82 <has_text text="8" />
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83 </assert_contents>
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84 </output>
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85 </test>
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86 </tests>
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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87 <help><![CDATA[
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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88
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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89 This module takes as input blast file from blast annotation and fasta contig file.
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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90 Set the right blast type or else the query overlap and hit overlap values will be wrong.
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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91 For TBLASTX type, the standard maximum evalue is 0.001.
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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92
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93 ]]></help>
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94 <expand macro="citations"/><!--rajouter ete3-->
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95 </tool>