Mercurial > repos > iuc > gff3_rebase

annotate gff3_rebase.xml @ 0:e54940ea270c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase commit 350ab347625ed5941873ba0deb3e1cf219d60052
author iuc
date Thu, 20 Apr 2017 08:12:49 -0400
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e54940ea270c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase commit 350ab347625ed5941873ba0deb3e1cf219d60052
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1 <tool id="gff3.rebase" name="Rebase GFF3 features" version="1.2">
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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 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>python gff3_rebase.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 python '$__tool_directory__/gff3_rebase.py'
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10 '$parent'
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11 '$child'
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12
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13 $interpro
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14 $protein2dna
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15 > '$output']]>
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16 </command>
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17 <inputs>
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18 <param label="Parent GFF3 annotations" name="parent" format="gff3" type="data"/>
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19 <param label="Child GFF3 annotations to rebase against parent" name="child" format="gff3" type="data"/>
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21 <param label="Interpro specific modifications" name="interpro" type="boolean" truevalue="--interpro" falsevalue=""/>
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22 <param label="Map protein translated results to original DNA data" name="protein2dna" type="boolean" truevalue="--protein2dna" falsevalue=""/>
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23 </inputs>
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24 <outputs>
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25 <data format="gff3" name="output"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="parent" value="parent.gff"/>
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30 <param name="child" value="child.gff"/>
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31 <param name="protein2dna" value="True" />
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32 <output name="output" file="proteins.gff"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **What it does**
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37
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38 Often the genomic data processing/analysis process requires a workflow like the following:
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39
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40 - select some features from a genome
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41 - export the sequences associated with those regions
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42 - analyse those exports with some tool like Blast
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43
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44 For display, especially in software like JBrowse, it is convenient to know
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45 where in the original genome the analysis results would fall. E.g. if a
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46 transmembrane domain is detected at bases 10-20 of an analysed protein, where
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47 should this be displayed relative to the parent genome?
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48
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49 This tool helps fill that gap, by rebasing some analysis results against the
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50 parent features which were originally analysed.
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51
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52 **Example Inputs**
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53
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54 For a "child" set of annotations like::
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55
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56 #gff-version 3
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57 cds42 blastp match_part 1 50 1e-40 . . ID=m00001;Notes=RNAse A Protein
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58
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59 And a parent set of annotations like::
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60
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61 #gff-version 3
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62 PhageBob maker cds 300 600 . + . ID=cds42
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63
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64 One could imagine that during the analysis process, the user had exported the parent annotation into some sequence::
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65
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66 >cds42
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67 M......
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68
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69 and then analysed those results, producing the "child" annotation file. This
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70 tool will then localize the results properly against the parent::
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71
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72 #gff-version 3
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73 PhageBob blastp match_part 300 449 1e-40 + . ID=m00001;Notes=RNAse A Protein
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74
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75 which will allow you to display the results in the correct location in visualizations.
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76
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77 **Options**
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78
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79 There are two optional flags which can be passed.
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80
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81 The Interpro flag selectively ignores features which shouldn't be included in
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82 the output (i.e. ``polypeptide``), and a couple of qualifiers that aren't
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83 useful (``status``, ``Target``)
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84
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85 The "Map Protein..." flag says that you translated the sequences during the
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86 genomic export process, analysing protein sequences. This indicates to the
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87 software that the bases should be multiplied by three to obtain the correct DNA
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88 locations.
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89 ]]></help>
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90 <citations>
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91 <citation type="doi">10.1093/bioinformatics/btp163</citation>
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92 </citations>
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93 </tool>