Mercurial > repos > iuc > homer_gtf_to_annotations

annotate homer_gtf_to_annotation.xml @ 1:debfd2838aca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
author iuc
date Sun, 26 Sep 2021 12:28:29 +0000
parents 8ebb6520eef4
children 7c5da353e460
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1 <tool id="homer_gtf_to_annotations" name="Converts GTF to Annotations file for Homer" version="@TOOL_VERSION@+galaxy0" profile="20.05">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements"/>
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6 <command detect_errors="exit_code"><![CDATA[
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7 ## Run parseGTF.pl
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8 parseGTF.pl $gtf_file ann
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9 ## Different options
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10 $type
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11 $id
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12 $removeAccVer
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13 $removeEnsemblVer
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14 -annTSSstartOffset $annTSSstartOffset
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15 -annTSSendOffset $annTSSendOffset
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16 -annTTSstartOffset $annTTSstartOffset
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17 -annTTSendOffset $annTTSendOffset
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18 #if $features != 'None':
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19 #set features_space = ' '.join(str($features).split(','))
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20 -features $features_space
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21 #end if
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22 > annotations.txt &&
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23 ## Prioritize and add intergenic annotation
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24 assignGenomeAnnotation annotations.txt annotations.txt -prioritize $output > $output_stats
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25 ]]></command>
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26 <inputs>
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27 <param name="gtf_file" type="data" format="gtf,gff,gff3" label="GTF file" help="Must be of datatype &quot;gtf&quot; or &quot;gff&quot; or &quot;gff3&quot;"/>
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28 <param name="type" type="select" label="Format of input file">
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29 <option value="">GTF</option>
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30 <option value="-gff">GFF (treats 9th column as ID)</option>
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31 <option value="-gff3">GFF3 (looks for parent attribute to assign gene name)</option>
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32 </param>
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33 <param name="id" type="select" label="Primary identifier">
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34 <option value="-tid">Transcript ID</option>
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35 <option value="-gid">Gene ID</option>
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36 </param>
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37 <param name="features" type="select" label="Which feature(s) to use?" multiple="true" display="checkboxes">
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38 <option value="exon" selected="true">exon</option>
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39 <option value="start_codon" selected="true">start_codon</option>
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40 <option value="stop_codon" selected="true">stop_codon</option>
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41 </param>
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42 <param name="removeAccVer" type="boolean" truevalue="-removeAccVer" falsevalue="" label="Remove any .1, .2, etc. at end of accession numbers, i.e. AT1G01040.2" help="-removeAccVer; Default=False"/>
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43 <param name="removeEnsemblVer" type="boolean" truevalue="-removeEnsemblVer" falsevalue="" label="Remove 'transcript:' and '_T01' style ids" help="-removeEnsemblVer; Default=False"/>
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44 <param name="annTSSstartOffset" type="integer" value="-1000" label="distance upstream of TSS to start promoter annotation" help="-annTSSstartOffset; Default=-1000"/>
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45 <param name="annTSSendOffset" type="integer" value="100" label="distance upstream/downstream of TSS to end promoter annotation" help="-annTSSendOffset; Default=100"/>
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46 <param name="annTTSstartOffset" type="integer" value="-100" label="distance upstream of TTS to start TTS annotation" help="-annTTSstartOffset; Default=-100"/>
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47 <param name="annTTSendOffset" type="integer" value="1000" label="distance upstream/downstream of TTS to end TTS annotation" help="-annTTSendOffset; Default=1000"/>
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48 </inputs>
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49 <outputs>
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50 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Annotations"/>
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51 <data format="tabular" name="output_stats" label="${tool.name} on ${on_string}: Annotation stats"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <!-- simple test with default -->
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56 <param name="gtf_file" value="small.gtf" ftype="gtf"/>
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57 <output name="output" file="annotations_default.txt" ftype="tabular"/>
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58 <output name="output_stats" file="annotations_default_stats.txt" ftype="tabular"/>
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59 </test>
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60 <test>
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61 <!-- simple test with default except no exon_end -->
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62 <param name="gtf_file" value="small.gtf" ftype="gtf"/>
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63 <param name="features" value="exon,start_codon"/>
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64 <output name="output" file="annotations_exon_start.txt" ftype="tabular"/>
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65 <output name="output_stats" file="annotations_exon_start_stats.txt" ftype="tabular"/>
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66 </test>
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67 <test>
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68 <!-- simple test with default smaller TSS TTS -->
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69 <param name="gtf_file" value="small.gtf" ftype="gtf"/>
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70 <param name="annTSSstartOffset" value="-50"/>
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71 <param name="annTSSendOffset" value="50"/>
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72 <param name="annTTSstartOffset" value="-50"/>
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73 <param name="annTTSendOffset" value="50"/>
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74 <output name="output" file="annotations_small_TSSTTS.txt" ftype="tabular"/>
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75 <output name="output_stats" file="annotations_small_TSSTTS_stats.txt" ftype="tabular"/>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 This tool convert a GTF file to a HOMER-style annotation file compatible with annotatePeaks.
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80 It follows the tutorial proposed here: http://homer.ucsd.edu/homer/ngs/advancedAnnotation.html
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81 ]]></help>
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82 <expand macro="citation"/>
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83 </tool>