Mercurial > repos > iuc > virannot_otu

annotate virAnnot_otu.xml @ 0:e924ab4ab00a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
author iuc
date Wed, 21 Aug 2024 13:13:10 +0000
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0
e924ab4ab00a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
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1 <tool id="virannot_otu" name="virAnnot OTU" version="1.0.1+galaxy0" profile="21.05">
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2 <description>create viral OTUs based on RPS and Blast annotations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <required_files>
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9 <include path="otu.py" />
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10 <include path="seek_otu.R" />
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11 <include path="rps2tree_html.py" />
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12 </required_files>
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13 <command detect_errors="aggressive"><![CDATA[
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14
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15 @HEADLESS@
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16 #if $blast_files
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17 #for $blast_file in $blast_files
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18 ln -fs '$blast_file' '$blast_file.element_identifier' &&
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19 #end for
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20 #end if
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21 #for $rps_file in $rps_files
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22 ln -fs '$rps_file' '$rps_file.element_identifier' &&
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23 #end for
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24 #for $fasta_file in $fasta_files
e924ab4ab00a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
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25 ln -fs '$fasta_file' '$fasta_file.element_identifier' &&
e924ab4ab00a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
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26 #end for
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27
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28 python '$__tool_directory__/otu.py'
e924ab4ab00a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
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29 #if $blast_files
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30 #for $blast_file in $blast_files
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31 -b '$blast_file.element_identifier'
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32 #end for
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33 #end if
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34 #for $rps_file in $rps_files
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35 -r '$rps_file.element_identifier'
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36 #end for
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37 #for $fasta_file in $fasta_files
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38 -f '$fasta_file.element_identifier'
e924ab4ab00a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
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39 #end for
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40 -p '$percentage'
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41 -vp '$viral_portion'
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42 -mpl '$min_prot_length'
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43 -tp '$__tool_directory__/'
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44 -o otu_output
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45
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46 && zip -r out.zip otu_output
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47
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48 ]]></command>
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49 <inputs>
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50 <param type="data" name="blast_files" format="tabular" label="Blast results file with taxonomy" multiple="true" optional="true"
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51 help="Give one file per sample. If a file is missing, give none." />
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52 <param type="data" name="rps_files" format="tabular" label="RPS results file" multiple="true" />
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53 <param type="data" name="fasta_files" format="fasta" label="Contigs file" multiple="true" />
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54 <param type="integer" name="percentage" label="Similarity threshold percentage for OTUs cutoff" value="90" min="10" max="100" />
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55 <param type="select" name="viral_portion" label="Minimun portion of viral sequences in RPS domain to be included">
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56 <option value="0.1">0.1</option>
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57 <option value="0.2">0.2</option>
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58 <option value="0.3" selected="true">0.3</option>
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59 <option value="0.4">0.4</option>
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60 <option value="0.5">0.5</option>
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61 </param>
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62 <param type="select" name="min_prot_length" label="Minimum query protein length">
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63 <option value="50">50</option>
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64 <option value="80">80</option>
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65 <option value="100" selected="true">100</option>
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66 <option value="150">150</option>
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67 <option value="200">200</option>
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68 </param>
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69 </inputs>
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70 <outputs>
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71 <data format="xlsx" name="otu_table" label="${tool.name} on ${on_string}: otu_stats" from_work_dir="otu_output/otu_stats.xlsx" />
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72 <data format="zip" name="archive_output" label="${tool.name} on ${on_string}: zip of the complete output" from_work_dir="out.zip" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="blast_files" value="otu_s1_tblastx.tab,otu_s2_tblastx.tab"/>
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77 <param name="rps_files" value="otu_s1_rps.tab,otu_s2_rps.tab"/>
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78 <param name="fasta_files" value="otu_s1.fa,otu_s2.fa"/>
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79 <param name="percentage" value="90"/>
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80 <param name="viral_portion" value="0.3"/>
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81 <param name="min_prot_length" value="100"/>
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82 <!-- check created zip -->
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83 <output name="archive_output">
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84 <assert_contents>
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85 <has_archive_member path=".*\/index.html" />
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86 <has_archive_member path=".*\/pfam00680_RdRP_1/seq_aligned.final_tree.fa" />
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87 </assert_contents>
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88 </output>
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92
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93 This module takes as input rps file from rps2tsv, blast file from blastxml_to_tabular [optional] and fasta contig file [optional].
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94
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95 If no blast file is given, OTUs will not have an associated annotation i.e the OTUs will be set as unknown.
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96 Files are processed in alphabetical order. Make sure that the files (blast, rps and contig) for a sample are named in the same way,
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97 otherwise they will be disassociated.
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98
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99 The standard similarity threshold is 90% [default value] which is a proxy to viral species compared with the ICTV classification.
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100
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101 ]]></help>
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102 <expand macro="citations" />
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103 </tool>