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author cpt
date Fri, 05 Jan 2024 05:52:31 +0000
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1 <tool id="gff3.rebase" name="Rebase GFF3 features" version="19.1.0.0">
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2 <description>against parent features</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command interpreter="python" detect_errors="aggressive"><![CDATA[gff3_rebase.py
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9 '$parent'
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10 '$child'
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11
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12 '$interpro'
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13 '$protein2dna'
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14 --map_by "$map_by"
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15 > '$default']]></command>
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16 <inputs>
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17 <param label="Parent GFF3 annotations" name="parent" format="gff3" type="data"/>
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18 <param label="Child GFF3 annotations to rebase against parent" name="child" format="gff3" type="data"/>
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19 <param label="Interpro specific modifications" name="interpro" type="boolean" truevalue="--interpro" falsevalue=""/>
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20 <param label="Map protein translated results to original DNA data" name="protein2dna" type="boolean" truevalue="--protein2dna" falsevalue=""/>
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21 <param label="Mapping Key" name="map_by" type="text" value="ID"/>
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22 </inputs>
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23 <outputs>
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24 <data format="gff3" name="default"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="parent" value="T7_CLEAN.gff3"/>
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29 <param name="child" value="T7_TMHMM.gff3"/>
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30 <param name="interpro" value=""/>
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31 <param name="protein2dna" value="--protein2dna"/>
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32 <param name="map_by" value="ID"/>
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33 <output name="default" file="T7_TMHMM_REBASE.gff3"/>
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34 </test>
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35 <test>
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36 <param name="parent" value="parent.gff"/>
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37 <param name="child" value="child.gff"/>
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38 <param name="interpro" value=""/>
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39 <param name="protein2dna" value="--protein2dna"/>
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40 <param name="map_by" value="ID"/>
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41 <output name="default" file="proteins.gff"/>
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42 </test>
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43 <test>
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44 <param name="parent" value="parent.gff"/>
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45 <param name="child" value="child.gff"/>
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46 <param name="interpro" value=""/>
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47 <param name="protein2dna" value=""/>
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48 <param name="map_by" value="ID"/>
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49 <output name="default" file="nonprotein.gff"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 **What it does**
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54
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55 The workflow in a genomic data analysis typically follows a process of feature
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56 export, analysis and then mapping the results of the analysis back to the genome.
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57
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58 For meaningful display in JBrowse, it is necessary to accurately map
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59 analysis results back to their corresponding positions in the context of the entire
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60 genome.
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61
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62 This tool fills that gap, by *rebasing* (calculating parent genome coordinates)
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63 features from analysis results against the parent features which
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64 were originally used for the analysis.
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65
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66 **Example Input/Output**
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67
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68 For a *parent* set of annotations::
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69
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70 #gff-version 3
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71 PhageBob maker cds 300 600 . + . ID=cds42
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72
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73 Where the analysis had exported the CDS (child) FASTA sequence::
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74
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75 >cds42
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76 MRTNASC
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77
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78 Then analyzed that feature, producing the *child* annotation file::
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79
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80 #gff-version 3
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81 cds42 blastp match_part 1 50 1e-40 . . ID=m00001;Notes=RNAse A Protein
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82
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83 This tool will then localize the results properly against the parent and permit
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84 proper visualization of the results in the correct location::
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85
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86 #gff-version 3
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87 PhageBob blastp match_part 300 449 1e-40 + . ID=m00001;Notes=RNAse A Protein
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88
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89 **Options**
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90
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91 The **Interpro specific modifications** option selectively ignores *features* (*i.e.* polypeptide) and
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92 qualifiers (status, Target) not needed in the output.
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93
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94 The **Map protein translated results to original DNA data** option indicates that the DNA sequences were translated into
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95 protein sequence during the genomic export process. When this option is selected,
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96 the tool will multiply the bases by three to obtain the correct DNA locations.
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97
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98 ]]></help>
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99 <expand macro="citations"/>
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100 </tool>