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1 <?xml version="1.0"?>
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2 <tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.0.1">
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3 <description>3 frame translation of BED augmented with a sequence column</description>
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1
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4 <requirements>
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5 <requirement type="package" version="1.62">biopython</requirement>
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6 <requirement type="python-module">Bio</requirement>
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7 </requirements>
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8 <command interpreter="python">translate_bed_sequences.py --input "$input"
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9 #if $reference:
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10 --reference $reference
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11 #else:
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12 --reference ${input.metadata.dbkey}
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13 #end if
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14 #if $seqtype:
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15 --seqtype $seqtype
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16 #end if
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17 #if $score_name:
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18 --score_name $score_name
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19 #end if
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20 #if $filter.filterseqs == 'yes':
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21 #if $filter.leading_bp:
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22 --leading_bp $filter.leading_bp
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23 #end if
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24 #if $filter.trailing_bp:
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25 --trailing_bp $filter.trailing_bp
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26 #end if
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27 #else:
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28 --unfiltered
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29 #end if
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30 #if $trim.trimseqs == 'no':
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31 --untrimmed
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32 #if $trim.max_stop_codons != None:
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33 --max_stop_codons $trim.max_stop_codons
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34 #end if
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35 #end if
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36 #if $min_length:
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37 --min_length $min_length
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38 #end if
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39 --output "$output"
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40 </command>
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41 <inputs>
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42 <param name="input" type="data" format="bed" label="BED file with added sequence column"
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43 help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/>
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44 <param name="reference" type="text" value="" optional="true" label="Genome reference name"
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45 help="By default, the database metadata will be used."/>
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46 <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
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47 help="For example: pep:novel"/>
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48 <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
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49 help="For example: with the tag name 'depth' and bed score 12: depth:12"/>
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50 <conditional name="filter">
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51 <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
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52 <option value="yes" selected="true">Yes</option>
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53 <option value="no">No</option>
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54 </param>
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55 <when value="yes">
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56 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs"
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57 help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>
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58 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs"
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59 help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>
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60 </when>
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61 <when value="no"/>
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62 </conditional>
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63 <conditional name="trim">
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64 <param name="trimseqs" type="select" label="Trim translations to stop codons">
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65 <option value="yes" selected="true">Yes</option>
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66 <option value="no">No</option>
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67 </param>
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68 <when value="no">
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69 <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/>
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70 </when>
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71 </conditional>
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72 <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>
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73 </inputs>
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74 <stdio>
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75 <exit_code range="1:" level="fatal" description="Error" />
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76 </stdio>
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77 <outputs>
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78 <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string}">
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79 <filter>'found' in str(outputs)</filter>
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80 </data>
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>
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85 <param name="reference" value="GRCh37"/>
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86 <param name="seqtype" value="pep:novel"/>
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87 <param name="score_name" value="depth"/>
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88 <output name="output" file="translated_bed_sequences.fa"/>
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89 </test>
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90 </tests>
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91 <help>
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92 **Translate BED Sequences**
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93
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94 This tool takes a BED input file that has been processed
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95 by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.
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96
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97 It generates a peptide fasta file with the 3-frame translations of the spliced sequence
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98 defined by each entry in the input BED file.
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99
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100
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101 </help>
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102 </tool>
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